Remove target mode variables and clean up pipeline

- Removed target mode specific files:
  - assets/schema_input_target.json
  - assets/samplesheet_example.csv
  - assets/target_samplesheet_example.csv
  - assets/design_examples/ directory
  - modules/local/generate_design_variants.nf

- Removed target mode test samplesheets:
  - assets/test_data/samplesheet_target_*.csv

- Updated documentation to remove target mode references:
  - docs/reference/parameters.md: Removed target mode parameters section
  - docs/architecture/implementation.md: Updated directory structure and validation examples
  - docs/getting-started/quick-reference.md: Simplified samplesheet templates and command recipes
  - docs/getting-started/usage.md: Updated design YAML template
  - docs/reference/examples.md: Complete rewrite with design mode examples only

- Kept only runnable test samplesheets:
  - samplesheet_design_nanobody.csv
  - samplesheet_design_peptide.csv
  - samplesheet_design_protein.csv

All target mode variables (min_length, max_length, length_step, n_variants_per_length,
design_type, target_chain_ids) have been removed from the pipeline. The pipeline now
operates exclusively in design mode using pre-made Boltzgen YAML specifications.

Author: Seqera AI

assets/design_examples/nanobody_design.yaml

@@ -43,9 +43,6 @@ nf-proteindesign/
 ├── workflows/
 │   └── protein_design.nf               # Unified workflow handling all modes
 ├── modules/local/
-│   ├── format_binding_sites.nf
-│   ├── generate_design_variants.nf
-│   ├── create_design_samplesheet.nf
 │   ├── boltzgen_run.nf
 │   ├── convert_cif_to_pdb.nf
 │   ├── collect_design_files.nf
@@ -60,11 +57,10 @@ nf-proteindesign/
 │   └── create_design_yaml.py          # Generate design YAML files
 └── assets/
     ├── schema_input_design.json        # Design mode samplesheet schema
-    ├── schema_input_target.json        # Target mode samplesheet schema
     └── test_data/                       # Test datasets
-        ├── designs/                     # Pre-made design YAMLs
-        ├── structures/                  # Test structures
-        └── samplesheets/                # Test samplesheets
+        ├── egfr_*_design.yaml          # Pre-made design YAMLs
+        ├── 2VSM.cif                     # Test structure
+        └── samplesheet_design_*.csv     # Test samplesheets
 ```
 
 ## :material-language-python: Helper Scripts
@@ -84,11 +80,7 @@ from pathlib import Path
 def validate_samplesheet(file_path):
     """Validate samplesheet CSV format."""
 
-    required_columns = ['sample']
-    mode_columns = {
-        'design': ['design_yaml'],
-        'target': ['target_structure'],
-    }
+    required_columns = ['sample_id', 'design_yaml']
 
     with open(file_path) as f:
         reader = csv.DictReader(f)
@@ -99,9 +91,7 @@ def validate_samplesheet(file_path):
             if col not in headers:
                 sys.exit(f"Missing required column: {col}")
 
-        # Detect mode
-        mode = detect_mode(headers)
-        print(f"Detected mode: {mode}")
+        print(f"Valid design mode samplesheet")
 
         return True
 
@@ -231,11 +221,11 @@ params {
 }
 
 def validateParameters() {
-    if (params.n_samples < 1) {
-        error "n_samples must be >= 1"
+    if (params.num_designs < 1) {
+        error "num_designs must be >= 1"
     }
-    if (params.max_length < params.min_length) {
-        error "max_length must be >= min_length"
+    if (params.budget < 1) {
+        error "budget must be >= 1"
     }
 }