From 24c22e1604bab1e5a58f4cc72b13f05a7081d808 Mon Sep 17 00:00:00 2001 From: Alex Thomas Date: Thu, 26 Oct 2023 14:34:15 +0000 Subject: [PATCH 1/2] more meaningful info --- workflow/scripts/generate-overview-table.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/scripts/generate-overview-table.py b/workflow/scripts/generate-overview-table.py index 448f61f1..3979a5a6 100644 --- a/workflow/scripts/generate-overview-table.py +++ b/workflow/scripts/generate-overview-table.py @@ -133,7 +133,7 @@ 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): From 231dab916047ae6fb1da7507bc092522f9a5e369 Mon Sep 17 00:00:00 2001 From: Alex Thomas Date: Mon, 6 Nov 2023 15:27:40 +0000 Subject: [PATCH 2/2] fmt --- workflow/scripts/generate-overview-table.py | 1 - 1 file changed, 1 deletion(-) diff --git a/workflow/scripts/generate-overview-table.py b/workflow/scripts/generate-overview-table.py index 3979a5a6..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",