Clean up main.nf: remove debug copy block and file listing

main.nf

@@ -55,16 +55,6 @@ process FLOWDOCK {
             auxiliary_estimation_only=false \\
             esmfold_chunk_size=null \\
             trainer=cpu 2>&1 | tee run.log
-        
-        # Copy any outputs from FlowDock's log directory if they exist there
-        if ls /software/flowdock/logs/sample/runs/*/rank*.pdb 2>/dev/null; then
-            cp /software/flowdock/logs/sample/runs/*/rank*.pdb ${params.sample_id}/ 2>/dev/null || true
-            cp /software/flowdock/logs/sample/runs/*/rank*.sdf ${params.sample_id}/ 2>/dev/null || true
-        fi
-        
-        # List what was generated
-        echo "=== Generated files ===" >> run.log
-        find ${params.sample_id}/ -type f >> run.log 2>&1 || true
         """
 }