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fix: more meaningful info for patient overview table #609

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merged 6 commits into from
Nov 22, 2023
Merged

fix: more meaningful info for patient overview table #609

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24c22e1
more meaningful info
alethomas Oct 26, 2023
bac9925
Merge branch 'master' into fix/minor
alethomas Nov 3, 2023
52a6804
Merge branch 'master' into fix/minor
alethomas Nov 6, 2023
231dab9
fmt
alethomas Nov 6, 2023
5bf21a3
Merge branch 'master' into fix/minor
alethomas Nov 13, 2023
dd41dfd
Merge branch 'master' into fix/minor
vBassewitz Nov 22, 2023
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3 changes: 1 addition & 2 deletions workflow/scripts/generate-overview-table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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):
Expand Down
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