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.

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"
-    outdir = "/omic/eureka/Pocketminer/output"
+    pdb = "s3://omic/eureka/Pocketminer/1HSG.pdb"
+    outdir = "s3://omic/eureka/Pocketminer/output"
     debug = false
 }