updating default value for phylo metadata headers

polio-nanopore · Oct 24, 2023 · d8eb66d · d8eb66d
1 parent a11affa
commit d8eb66d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/piranha/utils/config.py b/piranha/utils/config.py
@@ -65,7 +65,7 @@
 KEY_PHYLO_METADATA_COLUMNS = "phylo_metadata_columns"
 KEY_SUPPLEMENTARY_METADATA_COLUMNS = "supplementary_metadata_columns"
 
-VALUE_PHYLO_METADATA_COLUMNS = [KEY_DATE,KEY_EPID]
+VALUE_PHYLO_METADATA_COLUMNS = [KEY_VARIANT_COUNT,KEY_DATE,KEY_EPID]
 VALUE_SUPPLEMENTARY_METADATA_COLUMNS = ["location","lineage"]
 VALUE_SUPPLEMENTARY_METADATA_ID_COLUMN = "sequence_name"
 
@@ -123,7 +123,7 @@
 VALUE_OUTPUT_PREFIX = "analysis"
 VALUE_SUMMARY_HEADERS = ["taxon","sites","haplotype","num_reads","make_cns"]
 VALUE_REFERENCES_FOR_CNS = ["Sabin1-related","Sabin2-related","Sabin3-related","WPV1"]
-VALUE_PHYLO_HEADER = ["name","sample","barcode","source","reference_group"]
+VALUE_PHYLO_HEADER = ["name","sample","barcode","source","reference_group","variant_count"]
 
 VALUE_SAMPLE_TYPE = "stool"
 VALUE_ANALYSIS_MODE = "vp1"