From ea9cbfe5e7ecd94cfc7211d1f67dacab620f2bae Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sat, 8 May 2021 10:32:38 +0200
Subject: [PATCH] fix verbose arg
---
gga_get_data.py | 2 +-
gga_load_data.py | 2 +-
speciesData.py | 4 +++-
3 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/gga_get_data.py b/gga_get_data.py
index 8bc092d..80c6e37 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 c4ed559..6cc4b65 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 2d0ce21..f2b9702 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 = {}
--
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