fix: more meaningful info for patient overview table (#609)

* more meaningful info * fmt --------- Co-authored-by: vBassewitz <[email protected]>
IKIM-Essen · Nov 22, 2023 · 77f7960 · 77f7960
1 parent b232c00
commit 77f7960
Showing 1 changed file with 1 addition and 2 deletions.
diff --git 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):