Update test data (#108)

* Delete vignettes directory * Update flu_gisaid_metadata.csv
CDCgov · Jan 31, 2025 · a378898 · a378898
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diff --git a/test_data/FLU/flu_gisaid_metadata.csv b/test_data/FLU/flu_gisaid_metadata.csv
@@ -1,4 +1,4 @@
-sequence_name,gs-sample_name,organism,collection_date,authors,gs-Isolate_Name,gs-segment,gs-Subtype,gs-Lineage,gs-Passage_History,gs-Location,gs-province,gs-sub_province,gs-Location_Additional_info,gs-Host,gs-Host_Additional_info,gs-Sampling_Strategy,gs-Sequencing_Strategy,gs-Sequencing_Technology,gs-Assembly_Method,gs-Coverage,gs-Submitting_Sample_Id,gs-Originating_Lab_Id,gs-Originating_Sample_Id,gs-Antigen_Character,gs-Adamantanes_Resistance_geno,gs-Oseltamivir_Resistance_geno,gs-Zanamivir_Resistance_geno,gs-Peramivir_Resistance_geno,gs-Other_Resistance_geno,gs-Adamantanes_Resistance_pheno,gs-Oseltamivir_Resistance_pheno,gs-Zanamivir_Resistance_pheno,gs-Peramivir_Resistance_pheno,gs-Other_Resistance_pheno,gs-Host_Age,gs-Host_Age_Unit,gs-Host_Gender,gs-Health_Status,gs-Note,gs-PMID
+sequence_name,gs-sample_name,organism,collection_date,authors,gs-Isolate_Name,gs-segment,gs-Subtype,gs-Lineage,gs-Passage_History,gs-Location,gs-province,gs-sub_province,gs-Location_Additional_info,gs-Host,gs-Host_Additional_info,gs-Sampling_Strategy,gs-Sequencing_Strategy,gs-Sequencing_Technology,gs-Assembly_Method,gs-Coverage,gs-Submitting_Sample_Id,gs-Originating_Lab_Id,gs-Originating_Sample_Id,gs-Antigen_Character,gs-Adamantanes_Resistance_geno,gs-Oseltamivir_Resistance_geno,gs-Zanamivir_Resistance_geno,gs-Peramivir_Resistance_geno,gs-Other_Resistance_geno,gs-Adamantanes_Resistance_pheno,gs-Oseltamivir_Resistance_pheno,gs-Zanamivir_Resistance_pheno,gs-Peramivir_Resistance_pheno,gs-Other_Resistance_pheno,gs-Host_Age,gs-Host_Age_Unit,gs-Host_Sex,gs-Health_Status,gs-Note,gs-PMID
 XX-566912_PB2,A/California/566912/2016_PB2,Influenza A virus,2016-12-28,John Doe; Jane Doe;,A/California/566912/2016,PB2,H3N2,,Original,United States,California,,,Human,,Baseline surveillance,,Illumina,FluAssembler,100x,,3080,,,,,,,,,,,,,92,Y,F,Unknown,,
 XX-566912_PB1,A/California/566912/2016_PB1,Influenza A virus,2016-12-28,John Doe; Jane Doe;,A/California/566912/2016,PB1,H3N2,,Original,United States,California,,,Human,,Baseline surveillance,,Illumina,FluAssembler,100x,,3080,,,,,,,,,,,,,92,Y,F,Unknown,,
 XX-566912_PA,A/California/566912/2016_PA,Influenza A virus,2016-12-28,John Doe; Jane Doe;,A/California/566912/2016,PA,H3N2,,Original,United States,California,,,Human,,Baseline surveillance,,Illumina,FluAssembler,100x,,3080,,,,,,,,,,,,,92,Y,F,Unknown,,

diff --git a/vignettes/biosample_submission.Rmd b/vignettes/biosample_submission.Rmd