diff --git a/.gitignore b/.gitignore
index 6c7a0af..2c518a9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
 *.pyc
 test-results
 /.idea
+.github
\ No newline at end of file
diff --git a/ovo_proteindj/components/workflow_visualization_components.py b/ovo_proteindj/components/workflow_visualization_components.py
index 6a18899..b7e03d6 100644
--- a/ovo_proteindj/components/workflow_visualization_components.py
+++ b/ovo_proteindj/components/workflow_visualization_components.py
@@ -372,9 +372,10 @@ def visualize_binder_design_structure(design_id: str):
     # TODO use target spec for this
     # Note this assumes that the target chain is B in the RFdiffusion output PDB,
     # and that the residue numbers are same as in the input PDB
+    target_chain = workflow.get_target_chain()
     hotspot_selections = (
-        [h.replace(workflow.target_chain, "B") for h in workflow.get_hotspots().split(",")]
-        if workflow.get_hotspots() and workflow.target_chain
+        [h.replace(target_chain, "B") for h in workflow.get_hotspots().split(",")]
+        if workflow.get_hotspots() and target_chain
         else None
     )
 
diff --git a/ovo_proteindj/logic.py b/ovo_proteindj/logic.py
index 100cd7a..9864983 100644
--- a/ovo_proteindj/logic.py
+++ b/ovo_proteindj/logic.py
@@ -32,13 +32,37 @@ def process_workflow_results(job: DesignJob, callback: Callable = None) -> list[
     assert job.workflow.is_instance(models_proteindj.ProteinDJDesignWorkflow), (
         "This function expects a ProteinDJDesignWorkflow instance, got: {}".format(type(job.workflow).__name__)
     )
+    
+    # Get source directory
+    source_dir = scheduler.get_output_dir(job.job_id)
+    run_dir = os.path.join(source_dir, "run")
+    
+    # Auto-detect or use configured fold directory
+    fold_dir = job.workflow.params.get('fold_method', 'rfd')
+    
+    # Auto-detect or use configured sequence design directory
+    seq_dir = job.workflow.params.get('seq_method')
+    if not seq_dir:
+        for option in ["fampnn", "mpnn"]:
+            if os.path.exists(os.path.join(run_dir, option)):
+                seq_dir = option
+                break
+    
+    # Auto-detect or use configured structure prediction directory
+    pred_dir = job.workflow.params.get('pred_method')
+    if not pred_dir:
+        for option in ["af2", "boltz"]:
+            if os.path.exists(os.path.join(run_dir, option)):
+                pred_dir = option
+                break
+    
     return process_proteindj_output_dir(
         job=job,
         pool=pool,
-        source_dir=scheduler.get_output_dir(job.job_id),
-        fold_dir="rfd",
-        seq_dir=job.workflow.params.seq_method,
-        pred_dir=job.workflow.params.pred_method,
+        source_dir=source_dir,
+        fold_dir=fold_dir,
+        seq_dir=seq_dir,
+        pred_dir=pred_dir,
         callback=callback,
     )
 
diff --git a/ovo_proteindj/models_proteindj.py b/ovo_proteindj/models_proteindj.py
index 61f7081..d1d295e 100644
--- a/ovo_proteindj/models_proteindj.py
+++ b/ovo_proteindj/models_proteindj.py
@@ -14,7 +14,7 @@
 
 # Pipeline version
 # tag or commit ID from https://github.com/PapenfussLab/proteindj
-PIPELINE_VERSION = "5db7c4e6b9507ebfdcd20090ebb3eef544abe27c"
+PIPELINE_VERSION = "v2.1.1"
 
 # Get default pipeline params from OVO config
 plugin_config = config.plugins.get(__package__, {})