change keep_demographic_info to remove_demographic_info because less …

…confusing

bin/validate_metadata.py

@@ -33,7 +33,7 @@ def metadata_validation_main():
 	parameters_class.get_parameters()
 	parameters = parameters_class.parameters
 	try:
-		assert len([x for x in parameters.keys() if x in ['fasta_path', 'meta_path', 'output_dir', 'condaEnv', 'keep_demographic_info',
+		assert len([x for x in parameters.keys() if x in ['fasta_path', 'meta_path', 'output_dir', 'condaEnv', 'remove_demographic_info',
 														'date_format_flag', 'file_name', 'restricted_terms',
 														'illumina_instrument_restrictions', 'nanopore_instrument_restrictions',
 														'fasta_names', 'overwrite_output_files', 
@@ -122,9 +122,8 @@ def get_args():
 		parser.add_argument("-o", "--output_dir", type=str, default='validation_outputs',
 							help="Output Directory for final Files, default is current directory")
 		parser.add_argument("--overwrite_output_files", type=bool, default=True, help='whether to overwrite the output dir')
-		parser.add_argument("-k", "--keep_demographic_info", action="store_true", default=False,
-							help="Flag to keep potentially identifying demographic info if provided otherwise it will return an " +
-								 "error if personal information is provided." +
+		parser.add_argument("-k", "--remove_demographic_info", action="store_true", default=False,
+							help="Flag to remove potentially identifying demographic info if provided otherwise no change will be made " +
 								 "Applies to host_sex, host_age, race, ethnicity.")
 		parser.add_argument("-d", "--date_format_flag", type=str, default="s", choices=['s', 'o', 'v'],
 							help="Flag to differ date output, s = default (YYYY-MM), " +
@@ -320,13 +319,13 @@ def validate_main(self):
 					self.author_valid = False
 					self.sample_error_msg = "\n\t Invalid Author Name, please list as full names separated by ;"
 
-			# run the check on the PI meta information if the keep_demographic_info flag is true
+			# run the check on the PI meta information if the remove_demographic_info flag is true
 			try:
 				assert self.meta_case_grade is True
 			except AssertionError:
 				raise AssertionError(f'meta_case_grade was not reset to True')
-			if self.parameters['keep_demographic_info'] is False:
-				self.sample_error_msg += (f"\n\t\t'keep_demographic_info' flag is False. Sample demographic data will be removed if present.")
+			if self.parameters['remove_demographic_info'] is True:
+				self.sample_error_msg += (f"\n\t\t'remove_demographic_info' flag is True. Sample demographic data will be removed if present.")
 				self.metadata_df = self.check_meta_case(sample_info)
 
 			# check if the SRA submission is triggered, if it is, then run the class of functions for handling sra submission

conf/test_params.config

@@ -67,7 +67,7 @@ params {
         */
         val_output_dir                 = 'validation_outputs'
         date_format_flag               = 's'  // s = default (YYYY-MM), v = verbose(YYYY-MM-DD), o = original (leaves format unchanged)
-        keep_demographic_info          = false // if false, values in host_sex, host_age, race, ethnicity are set to 'Not Provided'
+        remove_demographic_info          = false // if true, values in host_sex, host_age, race, ethnicity are set to 'Not Provided'
         validate_custom_fields         = false
         custom_fields_file             = "${projectDir}/assets/custom_meta_fields/example_custom_fields.json"
 

modules/local/metadata_validation/main.nf

@@ -17,7 +17,7 @@ process METADATA_VALIDATION {
     input:
     path meta_path
 
-    def keep_demographic_info = params.keep_demographic_info == true ? '--keep_demographic_info' : ''
+    def remove_demographic_info = params.remove_demographic_info == true ? '--remove_demographic_info' : ''
     def validate_custom_fields = params.validate_custom_fields == true ? '--validate_custom_fields' : ''
 
     script:
@@ -27,7 +27,7 @@ process METADATA_VALIDATION {
         --output_dir . \
         --custom_fields_file $params.custom_fields_file \
         --date_format_flag $params.date_format_flag \
-        $keep_demographic_info $validate_custom_fields
+        $remove_demographic_info $validate_custom_fields
     """
 
     output:

nextflow.config

@@ -21,7 +21,7 @@ params {
 
     // validation subworkflow
     date_format_flag       = 's'  // s = default (YYYY-MM), v = verbose(YYYY-MM-DD), o = original (leaves format unchanged)
-    keep_demographic_info  = false // if false, values in host_sex, host_age, race, ethnicity are set to 'Not Provided'
+    remove_demographic_info  = false // if true, values in host_sex, host_age, race, ethnicity are set to 'Not Provided'
     validate_custom_fields = false
     custom_fields_file     = "${projectDir}/assets/custom_meta_fields/example_custom_fields.json"