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

main.nf

@@ -2,7 +2,6 @@
 
 nextflow.enable.dsl=2
 
-// Pipeline parameters
 params.pdb = 's3://omic/eureka/Pocketminer/1HSG.pdb'
 params.outdir = 's3://omic/eureka/Pocketminer/output'
 params.model_path = '/workspace/gvp/models/pocketminer'
@@ -22,66 +21,36 @@ process POCKETMINER {
         def debug_flag = params.debug ? '--debug' : ''
         def outdir = params.outdir
         """
-        set +e
-        touch run.log
         mkdir -p results
+        touch run.log
 
-        echo "=== Environment Debug ===" >> run.log
+        # Download input PDB from S3/MinIO
-        echo "Input path: ${pdb_path}" >> run.log
-        echo "Output path: ${outdir}" >> run.log
-
-        PDB_FILE=""
-
-        # Method 1: Direct path (if PVC mounted or local)
-        if [ -f "${pdb_path}" ]; then
-            echo "Found at direct path" >> run.log
-            cp "${pdb_path}" input.pdb && PDB_FILE="input.pdb"
-        fi
-
-        # Method 2: Convert s3://omic/... to /omic/... (PVC mount path)
-        if [ -z "\$PDB_FILE" ]; then
-            PVC_PATH="\$(echo '${pdb_path}' | sed 's|^s3://|/|')"
-            if [ -f "\$PVC_PATH" ]; then
-                echo "Found at PVC path: \$PVC_PATH" >> run.log
-                cp "\$PVC_PATH" input.pdb && PDB_FILE="input.pdb"
-            else
-                echo "Not found at PVC path: \$PVC_PATH" >> run.log
-            fi
-        fi
-
-        # Method 3: Download from MinIO using boto3
-        if [ -z "\$PDB_FILE" ]; then
-            ENDPOINT="\${AWS_ENDPOINT_URL:-http://datalake-hl.datalake.svc.cluster.local:9000}"
-            echo "Downloading via boto3 from: \$ENDPOINT" >> run.log
         python -c "
-import os, sys, boto3
+import os, boto3
 from botocore.client import Config
-s3_path = '${pdb_path}'.replace('s3://', '')
+
-bucket, key = s3_path.split('/', 1)
+def get_s3_client():
-endpoint = os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000')
+    return boto3.client('s3',
-print(f'Bucket: {bucket}, Key: {key}')
+        endpoint_url=os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000'),
-s3 = boto3.client('s3', endpoint_url=endpoint,
         aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', ''),
         aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', ''),
-    config=Config(signature_version='s3v4'), region_name='us-east-1')
+        config=Config(signature_version='s3v4'),
+        region_name='us-east-1')
+
+bucket, key = '${pdb_path}'.replace('s3://', '').split('/', 1)
+s3 = get_s3_client()
 s3.download_file(bucket, key, 'input.pdb')
-print(f'Downloaded {os.path.getsize(\"input.pdb\")} bytes')
+print(f'Downloaded input ({os.path.getsize(\"input.pdb\")} bytes)')
-" >> run.log 2>&1
+" 2>&1 | tee -a run.log
-            if [ -f input.pdb ] && [ -s input.pdb ]; then
-                PDB_FILE="input.pdb"
-            fi
-        fi
 
-        set -e
+        if [ ! -s input.pdb ]; then
-
+            echo "ERROR: Failed to download PDB file" | tee -a run.log
-        if [ -z "\$PDB_FILE" ] || [ ! -f input.pdb ]; then
-            echo "ERROR: Could not retrieve PDB file" >> run.log
-            cat run.log
             exit 1
         fi
 
         PDB_BASENAME="\$(basename '${pdb_path}' .pdb)"
 
+        # Run PocketMiner prediction
         python /workspace/entrypoint.py \\
             --pdb input.pdb \\
             --output-folder results \\
@@ -89,27 +58,28 @@ print(f'Downloaded {os.path.getsize(\"input.pdb\")} bytes')
             --model-path ${params.model_path} \\
             ${debug_flag} 2>&1 | tee -a run.log
 
-        # Upload results to S3
+        # Upload results to S3/MinIO
-        echo "Uploading results to ${outdir}..." >> run.log
         python -c "
 import os, boto3
 from botocore.client import Config
-outdir = '${outdir}'.replace('s3://', '')
+
-bucket, prefix = outdir.split('/', 1)
+def get_s3_client():
-endpoint = os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000')
+    return boto3.client('s3',
-s3 = boto3.client('s3', endpoint_url=endpoint,
+        endpoint_url=os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000'),
         aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', ''),
         aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', ''),
-    config=Config(signature_version='s3v4'), region_name='us-east-1')
+        config=Config(signature_version='s3v4'),
+        region_name='us-east-1')
+
+bucket, prefix = '${outdir}'.replace('s3://', '').split('/', 1)
+s3 = get_s3_client()
 for f in os.listdir('results'):
     filepath = os.path.join('results', f)
     if os.path.isfile(filepath):
         key = f'{prefix}/{f}'
         s3.upload_file(filepath, bucket, key)
         print(f'Uploaded {f} -> s3://{bucket}/{key}')
-" >> run.log 2>&1
+" 2>&1 | tee -a run.log
-
-        echo "Pipeline completed successfully" >> run.log
         """
 }
 

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'