diff --git a/scripts/plot_summary.py b/scripts/plot_summary.py index 48f064b0..bc2bd30c 100644 --- a/scripts/plot_summary.py +++ b/scripts/plot_summary.py @@ -21,7 +21,7 @@ Description import os import logging -from _helpers import configure_logging, retrieve_snakemake_keys +from _helpers import configure_logging import pandas as pd import matplotlib.pyplot as plt @@ -170,12 +170,12 @@ if __name__ == "__main__": attr='', ext='png', country='all') configure_logging(snakemake) - paths, config, wildcards, logs, out = retrieve_snakemake_keys(snakemake) + config = snakemake.config - summary = wildcards.summary + summary = snakemake.wildcards.summary try: func = globals()[f"plot_{summary}"] except KeyError: raise RuntimeError(f"plotting function for {summary} has not been defined") - func(os.path.join(paths[0], f"{summary}.csv"), config, out[0]) + func(os.path.join(snakemake.input[0], f"{summary}.csv"), config, snakemake.output[0])