Add multi-method input file resolution for WES

PVC mount is not available in k8s pods. Try multiple fallback
methods to retrieve input PDB: PVC path, s3-to-PVC conversion,
AWS CLI from MinIO, and curl from MinIO. Also add nf-amazon
plugin and s3:// default paths.

main.nf

@@ -3,8 +3,8 @@
 nextflow.enable.dsl=2
 
 // Pipeline parameters
-params.pdb = '/omic/eureka/Pocketminer/1HSG.pdb'
+params.pdb = 's3://omic/eureka/Pocketminer/1HSG.pdb'
-params.outdir = '/omic/eureka/Pocketminer/output'
+params.outdir = 's3://omic/eureka/Pocketminer/output'
 params.model_path = '/workspace/gvp/models/pocketminer'
 params.debug = false
 
@@ -25,30 +25,66 @@ process POCKETMINER {
         path "run.log", emit: log
 
     script:
-        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 "=== Environment Debug ===" | 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
+        echo "AWS_ENDPOINT_URL: \${AWS_ENDPOINT_URL:-not set}" | tee -a run.log
-        ls -la /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
+        echo "AWS_ACCESS_KEY_ID set: \${AWS_ACCESS_KEY_ID:+yes}" | tee -a run.log
-        echo "=== End Debug ===" | tee -a run.log
 
-        if [ ! -f "${pdb_path}" ]; then
+        # Try multiple methods to get the PDB file
-            echo "ERROR: PDB file not found at ${pdb_path}" | tee -a run.log
+        PDB_FILE=""
-            echo "Available files in /omic/eureka/Pocketminer/:" | tee -a run.log
+
-            ls /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
+        # Method 1: Direct PVC path (if mounted)
+        if [ -f "${pdb_path}" ]; then
+            echo "Found file at PVC path: ${pdb_path}" | tee -a run.log
+            cp "${pdb_path}" input.pdb
+            PDB_FILE="input.pdb"
+        fi
+
+        # Method 2: Convert s3://omic/eureka/... to /omic/eureka/... (PVC mount)
+        if [ -z "\$PDB_FILE" ]; then
+            PVC_PATH="\$(echo '${pdb_path}' | sed 's|^s3://|/|')"
+            echo "Trying PVC path: \$PVC_PATH" | tee -a run.log
+            if [ -f "\$PVC_PATH" ]; then
+                echo "Found file at PVC mount: \$PVC_PATH" | tee -a run.log
+                cp "\$PVC_PATH" input.pdb
+                PDB_FILE="input.pdb"
+            fi
+        fi
+
+        # Method 3: Download from MinIO via S3 API
+        if [ -z "\$PDB_FILE" ]; then
+            echo "PVC not available, downloading from MinIO S3..." | tee -a run.log
+            pip install awscli 2>/dev/null || conda install -n base -c conda-forge awscli -y 2>/dev/null || true
+
+            if command -v aws &> /dev/null; then
+                aws --endpoint-url \${AWS_ENDPOINT_URL:-http://datalake-hl.datalake.svc.cluster.local:9000} \\
+                    s3 cp "${pdb_path}" input.pdb 2>&1 | tee -a run.log && PDB_FILE="input.pdb"
+            fi
+        fi
+
+        # Method 4: Download via curl from MinIO
+        if [ -z "\$PDB_FILE" ]; then
+            echo "Trying curl download from MinIO..." | tee -a run.log
+            S3_PATH="\$(echo '${pdb_path}' | sed 's|^s3://||')"
+            curl -sf "http://datalake-hl.datalake.svc.cluster.local:9000/\$S3_PATH" -o input.pdb 2>&1 | tee -a run.log && PDB_FILE="input.pdb"
+        fi
+
+        if [ -z "\$PDB_FILE" ] || [ ! -f input.pdb ]; then
+            echo "ERROR: Could not retrieve PDB file from any source" | tee -a run.log
             exit 1
         fi
 
-        cp "${pdb_path}" input.pdb
+        echo "PDB file ready (\$(wc -c < input.pdb) bytes)" | tee -a run.log
+        PDB_BASENAME="\$(basename '${pdb_path}' .pdb)"
 
         python /workspace/entrypoint.py \\
             --pdb input.pdb \\
             --output-folder . \\
-            --output-name ${pdb_basename} \\
+            --output-name "\$PDB_BASENAME" \\
             --model-path ${params.model_path} \\
             ${debug_flag} 2>&1 | tee -a run.log
 

nextflow.config

@@ -8,10 +8,22 @@ manifest {
     version = '1.0.0'
 }
 
+// S3/MinIO plugin for direct S3 access (bypasses PVC mount issues)
+plugins {
+    id 'nf-amazon'
+}
+
+aws {
+    client {
+        endpoint = 'http://datalake-hl.datalake.svc.cluster.local:9000'
+        s3PathStyleAccess = true
+    }
+}
+
 // Global default parameters
 params {
-    pdb = "/omic/eureka/Pocketminer/1HSG.pdb"
+    pdb = "s3://omic/eureka/Pocketminer/1HSG.pdb"
-    outdir = "/omic/eureka/Pocketminer/output"
+    outdir = "s3://omic/eureka/Pocketminer/output"
     debug = false
 }