fix convertToStdVCF.py function to skip nonconventional headers

bin/convertToStdVCF.py

@@ -276,8 +276,16 @@ def extract_freestanding_columns_into_dict(line_original, col_indices, meta_info
     ]
 
     cols_as_INFO_dict = {}
+
     for column_name in columns_to_extract:
         if column_name not in col_indices:
+            print("Warning: '{}' not found in column indices.".format(column_name))
+            continue
+
+        column_index = col_indices[column_name]
+
+        if column_index >= len(line_original):
+            print("Warning: Column '{}' index {} is out of bounds in line: {}".format(column_name, column_index, line_original))
             continue
 
         old_column_contents = line_original[col_indices[column_name]]
@@ -548,4 +556,4 @@ def parse_options(argv):
         header =False
     else:
         header = args.raw_vcf      
-    convert(args.input_file, args.output_file, args.sample_id, meta_information,args.withcontrol,header)
+    convert(args.input_file, args.output_file, args.sample_id, meta_information, args.withcontrol, header)

nextflow.config

@@ -294,8 +294,8 @@ manifest {
     homePage        = 'https://github.com/kubranarci/nf-snvcalling'
     description     = 'ODCF SNV Calling pipeline'
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.10.3'
-    version         = '2.0.1'
+    nextflowVersion = '!>=23.10.1'
+    version         = '2.0.2'
 }
 // Nextflow plugins
 plugins {