Fix test profile parameter name mismatch and enable Foldseek

This commit addresses three issues identified in the test_design_protein profile:

1. **Parameter name mismatch**: Changed  to
   in all three test configs (test_design_protein, test_design_nanobody, test_design_peptide).
   The workflow code uses  but the test configs were using
   the wrong parameter name, causing Boltz2 refolding to be skipped.

2. **Enable Foldseek**: Changed  to  in
   test_design_protein config to enable structural similarity search in comprehensive testing.

3. **Verified workflow logic**: Confirmed that IPSAE, PRODIGY, and Foldseek modules
   correctly process both Boltzgen and Boltz2-refolded structures when the parameters
   are properly enabled.

Result: With these fixes, the test profiles will now properly:
- Run Boltz2 refolding on ProteinMPNN-optimized sequences
- Execute IPSAE and PRODIGY on both original and refolded structures
- Perform Foldseek structural similarity searches
- Generate comprehensive consolidated metrics reports

Files changed:
- conf/test_design_protein.config
- conf/test_design_nanobody.config
- conf/test_design_peptide.config

Author: Seqera AI

conf/test_design_nanobody.config

@@ -31,7 +31,7 @@ params {
     // Enable all metrics modules for comprehensive testing
     run_proteinmpnn            = true
     mpnn_num_seq_per_target    = 2     // Reduced from default 8 for faster testing
-    run_protenix_refold        = true
+    run_boltz2_refold          = true
     run_ipsae                  = true
     run_prodigy                = true
     run_foldseek               = true

conf/test_design_peptide.config

@@ -31,7 +31,7 @@ params {
     // Enable all metrics modules for comprehensive testing
     run_proteinmpnn            = true
     mpnn_num_seq_per_target    = 2     // Reduced from default 8 for faster testing
-    run_protenix_refold        = true
+    run_boltz2_refold          = true
     run_ipsae                  = true
     run_prodigy                = true
     run_foldseek               = true

conf/test_design_protein.config

@@ -31,10 +31,10 @@ params {
     // Enable all metrics modules for comprehensive testing
     run_proteinmpnn            = true
     mpnn_num_seq_per_target    = 2     // Reduced from default 8 for faster testing
-    run_protenix_refold        = true
+    run_boltz2_refold          = true
     run_ipsae                  = true
     run_prodigy                = true
-    run_foldseek               = false
+    run_foldseek               = true
     run_consolidation          = true
 
     // Output