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Commit ea9cbfe5 authored by Loraine Gueguen's avatar Loraine Gueguen
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fix verbose arg

parent 57ab77f5
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2 merge requests!9Release 2.0 (merge dev to master),!8Release 2.0
...@@ -200,7 +200,7 @@ if __name__ == "__main__": ...@@ -200,7 +200,7 @@ if __name__ == "__main__":
parser.add_argument("-v", "--verbose", parser.add_argument("-v", "--verbose",
help="Increase output verbosity", help="Increase output verbosity",
action="store_false") action="store_true")
parser.add_argument("--main-directory", parser.add_argument("--main-directory",
type=str, type=str,
......
...@@ -321,7 +321,7 @@ if __name__ == "__main__": ...@@ -321,7 +321,7 @@ if __name__ == "__main__":
parser.add_argument("-v", "--verbose", parser.add_argument("-v", "--verbose",
help="Increase output verbosity", help="Increase output verbosity",
action="store_false") action="store_true")
parser.add_argument("--config", parser.add_argument("--config",
type=str, type=str,
......
...@@ -93,6 +93,8 @@ class SpeciesData: ...@@ -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.api_key = None # API key used to communicate with the galaxy instance. Cannot be used to do user-tied actions
self.datasets = dict() self.datasets = dict()
self.config = None # Custom config used to set environment variables inside containers 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.existing_folders_cache = {}
self.bam_metadata_cache = {} self.bam_metadata_cache = {}
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