diff --git a/workflow/scripts/generate-overview-table.py b/workflow/scripts/generate-overview-table.py index 448f61f1..304cef0c 100644 --- a/workflow/scripts/generate-overview-table.py +++ b/workflow/scripts/generate-overview-table.py @@ -29,7 +29,6 @@ def is_patient_report(): # add kraken estimates species_columns = pd.DataFrame() for sample, file in iter_with_samples(snakemake.input.kraken): - kraken_results = pd.read_csv( file, delimiter="\t", @@ -133,7 +132,7 @@ def register_contig_lengths(assemblies, name): elif "consensus" == used: data.loc[sample, "Best Quality"] = "Consensus" elif "not-accepted" == used: - data.loc[sample, "Best Quality"] = "-" + data.loc[sample, "Best Quality"] = "not accepted by QA" # add pangolin results for sample, file in iter_with_samples(snakemake.input.pangolin):