Add early validation for duplicate experimental design combinations

bin/validate_expdesign.py

@@ -0,0 +1,121 @@
+#!/usr/bin/env python3
+"""
+Validates OpenMS experimental design files for duplicate (Fraction_Group, Fraction, Label) combinations.
+
+This script checks the experimental design file generated from SDRF conversion to ensure that
+each combination of (Fraction_Group, Fraction, Label) appears only once, which is a requirement
+for downstream OpenMS tools like MSstatsConverter and ProteinQuantifier.
+"""
+
+import sys
+import argparse
+import csv
+from collections import defaultdict
+
+
+def validate_expdesign(expdesign_file):
+    """
+    Validate the experimental design file for duplicate combinations.
+
+    Args:
+        expdesign_file: Path to the OpenMS experimental design TSV file
+
+    Returns:
+        bool: True if validation passes, False otherwise
+    """
+    print(f"Validating experimental design file: {expdesign_file}")
+
+    # Track combinations and their row numbers
+    combinations = defaultdict(list)
+
+    # Read the file
+    try:
+        with open(expdesign_file, 'r', encoding='utf-8') as f:
+            reader = csv.DictReader(f, delimiter='\t')
+
+            # Check if required columns exist
+            required_cols = ['Fraction_Group', 'Fraction', 'Label']
+            if not all(col in reader.fieldnames for col in required_cols):
+                print(f"ERROR: Missing required columns. Expected columns: {required_cols}")
+                print(f"Found columns: {reader.fieldnames}")
+                return False
+
+            # Check each row for duplicates
+            for row_num, row in enumerate(reader, start=2):  # Start at 2 because line 1 is header
+                fraction_group = row.get('Fraction_Group', '')
+                fraction = row.get('Fraction', '')
+                label = row.get('Label', '')
+
+                # Create the combination tuple
+                combination = (fraction_group, fraction, label)
+
+                # Track which rows have this combination
+                combinations[combination].append({
+                    'row': row_num,
+                    'data': row
+                })
+
+        # Check for duplicates
+        duplicates_found = False
+        for combination, occurrences in combinations.items():
+            if len(occurrences) > 1:
+                duplicates_found = True
+                fraction_group, fraction, label = combination
+                print(f"\nERROR: Duplicate (Fraction_Group={fraction_group}, Fraction={fraction}, Label={label}) combination found!")
+                print(f"This combination appears {len(occurrences)} times in the following rows:")
+
+                for occurrence in occurrences:
+                    row_num = occurrence['row']
+                    data = occurrence['data']
+                    # Get relevant columns for display
+                    sample = data.get('Sample', 'N/A')
+                    spectra = data.get('Spectra_Filepath', data.get('MSRun', 'N/A'))
+                    print(f"  - Row {row_num}: Sample={sample}, Spectra={spectra}")
+
+        if duplicates_found:
+            print("\n" + "="*80)
+            print("VALIDATION FAILED: Duplicate (Fraction_Group, Fraction, Label) combinations detected!")
+            print("="*80)
+            print("\nPlease fix the SDRF file to ensure each (Fraction_Group, Fraction, Label) combination is unique.")
+            print("Common causes:")
+            print("  - Duplicate label assignments for the same data file")
+            print("  - Incorrect fraction or fraction group assignments")
+            print("  - Copy-paste errors in the SDRF file")
+            return False
+        else:
+            print(f"\n✓ Validation passed: All {len(combinations)} (Fraction_Group, Fraction, Label) combinations are unique.")
+            return True
+
+    except FileNotFoundError:
+        print(f"ERROR: File not found: {expdesign_file}")
+        return False
+    except Exception as e:
+        print(f"ERROR: Failed to read or parse the file: {e}")
+        return False
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Validate OpenMS experimental design files for duplicate combinations',
+        formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+    parser.add_argument(
+        '--expdesign',
+        required=True,
+        help='Path to the OpenMS experimental design TSV file'
+    )
+
+    args = parser.parse_args()
+
+    # Run validation
+    is_valid = validate_expdesign(args.expdesign)
+
+    # Exit with appropriate code
+    if is_valid:
+        sys.exit(0)
+    else:
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    main()

modules/local/preprocess_expdesign/main.nf

@@ -27,13 +27,16 @@ process PREPROCESS_EXPDESIGN {
     # we edit the design here and change the endings.
     sed 's/.raw\\t/.mzML\\t/I' ${design} > ${design.baseName}_openms_design.tsv
 
+    # Validate the experimental design for duplicate combinations
+    quantmsutilsc validateexpdesign --expdesign ${design.baseName}_openms_design.tsv 2>&1 | tee validation.log
+
     # here we extract the filenames and fake an empty config (since the config values will be deduced from the workflow params)
     a=\$(grep -n '^\$' ${design} | head -n 1 | awk -F ":" '{print \$1}')
     sed -e ''"\${a}"',\$d' ${design} > ${design.baseName}_config.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sdrf-pipelines: \$(parse_sdrf --version 2>/dev/null | awk -F ' ' '{print \$2}')
+        quantms-utils: \$(pip show quantms-utils | grep "Version" | awk -F ': ' '{print \$2}')
     END_VERSIONS
     """
 }

modules/local/sdrf_parsing/main.nf

@@ -37,6 +37,9 @@ process SDRF_PARSING {
     mv openms.tsv ${sdrf.baseName}_config.tsv
     mv experimental_design.tsv ${sdrf.baseName}_openms_design.tsv
 
+    # Validate the experimental design for duplicate combinations
+    validate_expdesign.py --expdesign ${sdrf.baseName}_openms_design.tsv 2>&1 | tee -a ${sdrf.baseName}_parsing.log
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         sdrf-pipelines: \$(parse_sdrf --version 2>/dev/null | awk -F ' ' '{print \$2}')