From d8eb66da539eb64c4df0cafb7ea36307f0b1d791 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Tue, 24 Oct 2023 14:28:48 +0100 Subject: [PATCH] updating default value for phylo metadata headers --- piranha/utils/config.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/piranha/utils/config.py b/piranha/utils/config.py index 45aed1b..c9ae420 100644 --- 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"