diff --git a/gga_get_data.py b/gga_get_data.py index 8bc092de24dbcbef9d5a5725637fdeae2841d719..80c6e379027569b2c68e85cb06e17fc29c4fedfa 100755 --- a/gga_get_data.py +++ b/gga_get_data.py @@ -200,7 +200,7 @@ if __name__ == "__main__": parser.add_argument("-v", "--verbose", help="Increase output verbosity", - action="store_false") + action="store_true") parser.add_argument("--main-directory", type=str, diff --git a/gga_load_data.py b/gga_load_data.py index c4ed5594a9d3d173bd11d4ee4918a1152cd6a5ca..6cc4b65e70e7c03df7beb96d013095b6b69c367c 100755 --- a/gga_load_data.py +++ b/gga_load_data.py @@ -321,7 +321,7 @@ if __name__ == "__main__": parser.add_argument("-v", "--verbose", help="Increase output verbosity", - action="store_false") + action="store_true") parser.add_argument("--config", type=str, diff --git a/speciesData.py b/speciesData.py index 2d0ce2157495e15af853053e602ce674b299a68d..f2b97026d4d929a39e21c79b31058f498f253622 100755 --- a/speciesData.py +++ b/speciesData.py @@ -93,6 +93,8 @@ class SpeciesData: self.api_key = None # API key used to communicate with the galaxy instance. Cannot be used to do user-tied actions self.datasets = dict() self.config = None # Custom config used to set environment variables inside containers - self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase.lower(), self.species.lower(), self.strain.lower(), self.sex.lower()])["not_empty"]) + self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items( + [self.genus_lowercase.lower(), self.species.lower(), self.strain.lower(), + self.sex.lower()])["not_empty"]) self.existing_folders_cache = {} self.bam_metadata_cache = {}