From a1c2896b83f2984999120480006c5f657fa0caaf Mon Sep 17 00:00:00 2001 From: aineniamh Date: Fri, 8 Apr 2022 10:25:21 +0100 Subject: [PATCH] issue #420 catching print out from versions and alias ordering issue --- pangolin/command.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pangolin/command.py b/pangolin/command.py index 86d0340..33e991e 100644 --- a/pangolin/command.py +++ b/pangolin/command.py @@ -142,9 +142,6 @@ def main(sysargs = sys.argv[1:]): # Parsing analysis mode flags to return one of 'usher' or 'pangolearn' config[KEY_ANALYSIS_MODE] = set_up_analysis_mode(args.analysis_mode, config[KEY_ANALYSIS_MODE]) - print(green(f"****\nPangolin running in {config[KEY_ANALYSIS_MODE]} mode.\n****")) - if config[KEY_ANALYSIS_MODE] == "scorpio": - print(cyan(f"Warning: in `scorpio` mode only variants of concern (VOCs) defined in constellations can be assigned. `Version` column corresponds to constellation_version.\n")) snakefile = get_snakefile(thisdir,config[KEY_ANALYSIS_MODE]) @@ -159,6 +156,9 @@ def main(sysargs = sys.argv[1:]): # by allowing query to accept 0 to many arguments print(green(f"****\nPangolin running in {config[KEY_ANALYSIS_MODE]} mode.\n****")) + if config[KEY_ANALYSIS_MODE] == "scorpio": + print(cyan(f"Warning: in `scorpio` mode only variants of concern (VOCs) defined in constellations can be assigned. `Version` column corresponds to constellation_version.\n")) + print_ram_warning(config[KEY_ANALYSIS_MODE]) # setup outdir and outfiles