change default value of working_directory

mehrdadbakhtiari · Mar 27, 2019 · 6985272 · 6985272
1 parent 5700f0d
commit 6985272
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diff --git a/advntr/__main__.py b/advntr/__main__.py
@@ -72,7 +72,7 @@ def main():
     genotype_others_group = genotype_parser.add_argument_group("Other options")
     genotype_others_group.add_argument('-h', '--help', action='help',
                                        help='show this help message and exit')
-    genotype_others_group.add_argument('--working_directory', type=str, metavar='<path>',
+    genotype_others_group.add_argument('--working_directory', type=str, metavar='<path>', default=None,
                                        help='working directory for creating temporary files needed for computation')
     genotype_others_group.add_argument('-m', '--models', type=str, metavar='<file>', default=None,
                                        help='VNTR models file [%s]' % settings.ILLUMINA_DEFAULT_MODELS_FILE)

diff --git a/advntr/advntr_commands.py b/advntr/advntr_commands.py
@@ -81,6 +81,8 @@ def genotype(args, genotype_parser):
     input_is_alignment_file = input_file.endswith('bam') or input_file.endswith('sam') or input_file.endswith('cram')
     if not input_is_alignment_file:
         print_error(genotype_parser, "The input file format is not supported. Please use BAM/CRAM files.")
+    if args.working_directory is None:
+        print_error(genotype_parser, 'Please specify working directory by -wd or --working_directory')
     working_directory = args.working_directory + '/' if args.working_directory else os.path.dirname(input_file) + '/'
 
     log_file = working_directory + 'log_%s.log' % os.path.basename(input_file)