From 14091fce875e59604392f6fcbe456ee8d4f47303 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 23 Mar 2026 15:27:23 +0100
Subject: [PATCH] Match meta-predictor's working WES pattern

- Add executor, docker, k8s storage config to k8s profile
- Use val input instead of file channel (avoids S3 staging issue)
- Pass PDB path as string, copy from PVC mount inside script
- Add PVC mount debug logging
- Set default params to /omic/eureka paths
---
 main.nf         | 64 +++++++++++++++++++++++++++++++------------------
 nextflow.config | 28 ++++++++++------------
 2 files changed, 54 insertions(+), 38 deletions(-)

diff --git a/main.nf b/main.nf
index ad36f6c..d7d4057 100644
--- a/main.nf
+++ b/main.nf
@@ -2,42 +2,60 @@
 
 nextflow.enable.dsl=2
 
-// Parameters
-params.pdb = null
-params.outdir = null
+// Pipeline parameters
+params.pdb = '/omic/eureka/Pocketminer/1HSG.pdb'
+params.outdir = '/omic/eureka/Pocketminer/output'
 params.model_path = '/workspace/gvp/models/pocketminer'
 params.debug = false
 
-// Process definition
 process POCKETMINER {
     container 'harbor.cluster.omic.ai/omic/pocketminer:latest'
     publishDir params.outdir, mode: 'copy'
 
     input:
-    path pdb_file
+        val pdb_path
 
     output:
-    path "*-preds.npy", emit: predictions_npy
-    path "*-predictions.txt", emit: predictions_txt
-    path "*-summary.json", emit: summary
-    path "*_X.npy", optional: true, emit: features_debug
-    path "*_S.npy", optional: true, emit: sequence_debug
-    path "*_mask.npy", optional: true, emit: mask_debug
+        path "*-preds.npy", emit: predictions_npy
+        path "*-predictions.txt", emit: predictions_txt
+        path "*-summary.json", emit: summary
+        path "*_X.npy", optional: true, emit: features_debug
+        path "*_S.npy", optional: true, emit: sequence_debug
+        path "*_mask.npy", optional: true, emit: mask_debug
+        path "run.log", emit: log
 
     script:
-    def pdb_basename = pdb_file.baseName
-    def debug_flag = params.debug ? '--debug' : ''
-    """
-    python /workspace/entrypoint.py \\
-        --pdb ${pdb_file} \\
-        --output-folder . \\
-        --output-name ${pdb_basename} \\
-        --model-path ${params.model_path} \\
-        ${debug_flag}
-    """
+        def pdb_basename = file(pdb_path).baseName
+        def debug_flag = params.debug ? '--debug' : ''
+        """
+        touch run.log
+
+        echo "=== Debugging PVC mount ===" | tee -a run.log
+        echo "Input path: ${pdb_path}" | tee -a run.log
+        ls -la /omic/eureka/ 2>&1 | head -20 | tee -a run.log
+        ls -la /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
+        echo "=== End Debug ===" | tee -a run.log
+
+        if [ ! -f "${pdb_path}" ]; then
+            echo "ERROR: PDB file not found at ${pdb_path}" | tee -a run.log
+            echo "Available files in /omic/eureka/Pocketminer/:" | tee -a run.log
+            ls /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
+            exit 1
+        fi
+
+        cp "${pdb_path}" input.pdb
+
+        python /workspace/entrypoint.py \\
+            --pdb input.pdb \\
+            --output-folder . \\
+            --output-name ${pdb_basename} \\
+            --model-path ${params.model_path} \\
+            ${debug_flag} 2>&1 | tee -a run.log
+
+        echo "Pipeline completed successfully" | tee -a run.log
+        """
 }
 
-// Workflow
 workflow {
-    POCKETMINER(Channel.of(file(params.pdb)))
+    POCKETMINER(params.pdb)
 }
diff --git a/nextflow.config b/nextflow.config
index 5306e63..ad0ad98 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -8,36 +8,34 @@ manifest {
     version = '1.0.0'
 }
 
-// S3/MinIO plugin for direct S3 access
-plugins {
-    id 'nf-amazon'
-}
-
-aws {
-    client {
-        endpoint = 'http://datalake-hl.datalake.svc.cluster.local:9000'
-        s3PathStyleAccess = true
-    }
-}
-
 // Global default parameters
 params {
-    pdb = null
-    outdir = null
+    pdb = "/omic/eureka/Pocketminer/1HSG.pdb"
+    outdir = "/omic/eureka/Pocketminer/output"
     debug = false
 }
 
+// Profiles for different execution environments
 profiles {
     standard {
         docker {
             enabled = true
-            runOptions = '--rm'
+            temp = 'auto'
         }
     }
+
     k8s {
         process {
+            executor = 'k8s'
             container = 'harbor.cluster.omic.ai/omic/pocketminer:latest'
         }
+        docker {
+            enabled = true
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+        }
     }
 }