Clean up pipeline configuration

- Remove debug logging and dead PVC/direct-path fallbacks from main.nf
- Remove nf-amazon plugin and PVC storage config from nextflow.config
  (S3 access is handled by boto3 in the script)
- Simplify input download and output upload to single boto3 blocks

nextflow.config

@@ -1,4 +1,3 @@
-// Manifest for Nextflow metadata
 manifest {
     name = 'pocketminer-Nextflow'
     author = 'Olamide'
@@ -8,26 +7,12 @@ 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 = "s3://omic/eureka/Pocketminer/1HSG.pdb"
     outdir = "s3://omic/eureka/Pocketminer/output"
     debug = false
 }
 
-// Profiles for different execution environments
 profiles {
     standard {
         docker {
@@ -44,14 +29,9 @@ profiles {
         docker {
             enabled = true
         }
-        k8s {
-            storageClaimName = 'eureka-pvc'
-            storageMountPath = '/omic/eureka'
-        }
     }
 }
 
-// Process configurations
 process {
     cpus = 2
     memory = '8 GB'