updating scorpio call for all VOCs and VUIs, andf fixing cyan bug

pangolin/__init__.py

@@ -1,5 +1,5 @@
 _program = "pangolin"
-__version__ = "3.0.2"
+__version__ = "3.0.3"
 
 
 __all__ = [

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:

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):

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"]: