diff --git a/pangolin/__init__.py b/pangolin/__init__.py index bb84e16..568cf6e 100644 --- a/pangolin/__init__.py +++ b/pangolin/__init__.py @@ -1,5 +1,5 @@ _program = "pangolin" -__version__ = "3.0.2" +__version__ = "3.0.3" __all__ = [ diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk index 4fccb0b..59ecfa5 100644 --- a/pangolin/scripts/pangolearn.smk +++ b/pangolin/scripts/pangolearn.smk @@ -156,8 +156,7 @@ rule scorpio: -i {input.fasta:q} \ -o {output.report:q} \ -t {workflow.cores} \ - -n B.1.1.7 B.1.351 P.1 \ - --long > {log} + --long &> {log} """ rule generate_report: diff --git a/pangolin/utils/data_install_checks.py b/pangolin/utils/data_install_checks.py index fd8f873..3c4689a 100644 --- a/pangolin/utils/data_install_checks.py +++ b/pangolin/utils/data_install_checks.py @@ -1,6 +1,6 @@ #!/usr/bin/env python3 import pkg_resources -from pangolin.utils import log_colours as colour +from pangolin.utils.log_colours import green,cyan,red import sys import os @@ -11,7 +11,7 @@ def package_data_check(filename,directory,key,config): data = pkg_resources.resource_filename('pangolin', package_datafile) config[key] = data except: - sys.stderr.write(colour.cyan(f'Error: Missing package data.')+f'\n\t- {filename}\nPlease install the latest pangolin version with `pangolin --update`.\n') + sys.stderr.write(cyan(f'Error: Missing package data.')+f'\n\t- {filename}\nPlease install the latest pangolin version with `pangolin --update`.\n') sys.exit(-1) def get_snakefile(thisdir): diff --git a/pangolin/utils/dependency_checks.py b/pangolin/utils/dependency_checks.py index a7e9eac..0a25c15 100644 --- a/pangolin/utils/dependency_checks.py +++ b/pangolin/utils/dependency_checks.py @@ -2,7 +2,7 @@ import subprocess import os import sys -from pangolin.utils import log_colours as colour +from pangolin.utils.log_colours import green,cyan,red import importlib import pangolin.utils.custom_logger as custom_logger @@ -52,7 +52,7 @@ def check_dependencies(): sys.stderr.write(cyan(f'Error: Missing dependencies.')+f'\n{dependencies}Please update your pangolin environment.\n') sys.exit(-1) else: - print(colour.green("All dependencies satisfied.")) + print(green("All dependencies satisfied.")) def set_up_verbosity(config): if config["verbose"]: