I tested the scripts. Please change the code according to the following.
Change the filename of rule_ov_run.py to Snakefile so that it can be run automatically with snakemake command.
wrapper.py is not using the annotator and reporter parameters given by rule_ov_run.py. But then, wrapper.py is not needed for this example. Modify Snakefile so that wrapper.py is not needed.
Add output field to Snakefile. The output filenames are exampleinput.xlsx and exampleinput.vcf.
I tested the scripts. Please change the code according to the following.
rule_ov_run.pytoSnakefileso that it can be run automatically withsnakemakecommand.Snakefileso that wrapper.py is not needed.outputfield toSnakefile. The output filenames areexampleinput.xlsxandexampleinput.vcf.