From 01b157feec9b7d7d77c3d3b5923dfbbb35ef9a23 Mon Sep 17 00:00:00 2001
From: Rhiannon Cameron <48695054+cmrn-rhi@users.noreply.github.com>
Date: Tue, 3 May 2022 14:15:37 -0700
Subject: [PATCH] covid19 exampleInput 0.15.5

Updated example input to reflect recent changes in 0.15.5
---
 .../canada_covid19/exampleInput/README.md     |   2 +-
 ..._0-15-4.csv => invalidTestData_0-15-5.csv} |   6 +++---
 .../exampleInput/validTestData_0-15-4.xlsx    | Bin 33110 -> 0 bytes
 ...ta_0-15-4.csv => validTestData_0-15-5.csv} |   2 +-
 ...ta_0-15-4.tsv => validTestData_0-15-5.tsv} |   2 +-
 ...ta_0-15-4.xls => validTestData_0-15-5.xls} | Bin 21504 -> 21504 bytes
 .../exampleInput/validTestData_0-15-5.xlsx    | Bin 0 -> 12908 bytes
 7 files changed, 6 insertions(+), 6 deletions(-)
 rename template/canada_covid19/exampleInput/{invalidTestData_0-15-4.csv => invalidTestData_0-15-5.csv} (63%)
 delete mode 100644 template/canada_covid19/exampleInput/validTestData_0-15-4.xlsx
 rename template/canada_covid19/exampleInput/{validTestData_0-15-4.csv => validTestData_0-15-5.csv} (62%)
 rename template/canada_covid19/exampleInput/{validTestData_0-15-4.tsv => validTestData_0-15-5.tsv} (62%)
 rename template/canada_covid19/exampleInput/{validTestData_0-15-4.xls => validTestData_0-15-5.xls} (92%)
 create mode 100644 template/canada_covid19/exampleInput/validTestData_0-15-5.xlsx

diff --git a/template/canada_covid19/exampleInput/README.md b/template/canada_covid19/exampleInput/README.md
index 5167b231..f7f43816 100644
--- a/template/canada_covid19/exampleInput/README.md
+++ b/template/canada_covid19/exampleInput/README.md
@@ -1,7 +1,7 @@
 # CanCOGeN Example Input Data
 This directory contains example input/test data for the Canadian COVID Genomics Network (CanCOGeN) DataHarmonizer application template: `CanCOGeN Covid-19`. This data is appropriate for testing up to the version appended to the end of the file name, for example:
 
-- `validTestData_0-15-4.csv` is _valid_ for version `0.15.4` of the DataHarmonizer.
+- `validTestData_0-15-5.csv` is _valid_ for version `0.15.5` of the DataHarmonizer.
 
 ## Valid Test Data
 
diff --git a/template/canada_covid19/exampleInput/invalidTestData_0-15-4.csv b/template/canada_covid19/exampleInput/invalidTestData_0-15-5.csv
similarity index 63%
rename from template/canada_covid19/exampleInput/invalidTestData_0-15-4.csv
rename to template/canada_covid19/exampleInput/invalidTestData_0-15-5.csv
index c837fc92..a9dd3743 100644
--- a/template/canada_covid19/exampleInput/invalidTestData_0-15-4.csv
+++ b/template/canada_covid19/exampleInput/invalidTestData_0-15-5.csv
@@ -1,5 +1,5 @@
 Database Identifiers,,,,,,,,,,,,Sample collection and processing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Host Information,,,,,,,,,,,,,,,,,Host vaccination information,,,,,,,,,,,Host exposure information,,,,,,,,,,,,,,Host reinfection information,,,,,,Sequencing,,,,,,,,,,,,Bioinformatics and QC metrics,,,,,,,,,,,,,,,,,,,,,Lineage and Variant information,,,,,,Pathogen diagnostic testing,,,,,,,,,Contributor acknowledgement,
 specimen collector sample ID,third party lab service provider name,third party lab sample ID,case ID,Related specimen primary ID,IRIDA sample name,umbrella bioproject accession,bioproject accession,biosample accession,SRA accession,GenBank accession,GISAID accession,sample collected by,sample collector contact email,sample collector contact address,sequence submitted by,sequence submitter contact email,sequence submitter contact address,sample collection date,sample collection date precision,sample received date,geo_loc_name (country),geo_loc_name (state/province/territory),geo_loc_name (city),organism,isolate,purpose of sampling,purpose of sampling details,NML submitted specimen type,Related specimen relationship type,anatomical material,anatomical part,body product,environmental material,environmental site,collection device,collection method,collection protocol,specimen processing,specimen processing details,lab host,passage number,passage method,biomaterial extracted,host (common name),host (scientific name),host health state,host health status details,host health outcome,host disease,host age,host age unit,host age bin,host gender,host residence geo_loc name (country),host residence geo_loc name (state/province/territory),host subject ID,symptom onset date,signs and symptoms,pre-existing conditions and risk factors,complications,host vaccination status,number of vaccine doses received,vaccination dose 1 vaccine name,vaccination dose 1 vaccination date,vaccination dose 2 vaccine name,vaccination dose 2 vaccination date,vaccination dose 3 vaccine name,vaccination dose 3 vaccination date,vaccination dose 4 vaccine name,vaccination dose 4 vaccination date,vaccination history,location of exposure geo_loc name (country),destination of most recent travel (city),destination of most recent travel (state/province/territory),destination of most recent travel (country),most recent travel departure date,most recent travel return date,travel point of entry type,border testing test day type,travel history,exposure event,exposure contact level,host role,exposure setting,exposure details,prior SARS-CoV-2 infection,prior SARS-CoV-2 infection isolate,prior SARS-CoV-2 infection date,prior SARS-CoV-2 antiviral treatment,prior SARS-CoV-2 antiviral treatment agent,prior SARS-CoV-2 antiviral treatment date,purpose of sequencing,purpose of sequencing details,sequencing date,library ID,amplicon size,library preparation kit,flow cell barcode,sequencing instrument,sequencing protocol name,sequencing protocol,sequencing kit number,amplicon pcr primer scheme,raw sequence data processing method,dehosting method,consensus sequence name,consensus sequence filename,consensus sequence filepath,consensus sequence software name,consensus sequence software version,breadth of coverage value,depth of coverage value,depth of coverage threshold,r1 fastq filename,r2 fastq filename,r1 fastq filepath,r2 fastq filepath,fast5 filename,fast5 filepath,number of base pairs sequenced,consensus genome length,Ns per 100 kbp,reference genome accession,bioinformatics protocol,lineage/clade name,lineage/clade analysis software name,lineage/clade analysis software version,variant designation,variant evidence,variant evidence details,gene name 1,diagnostic pcr protocol 1,diagnostic pcr Ct value 1,gene name 2,diagnostic pcr protocol 2,diagnostic pcr Ct value 2,gene name 3,diagnostic pcr protocol 3,diagnostic pcr Ct value 3,authors,DataHarmonizer provenance
-sample123,Switch Health,abc12345,case4444,NMLsample2222,prov_rona_99,PRJNA623807,PRJNA608651,SAMN14180202,SRR11177792,MN908947.3,EPI_ISL_436489,,switch@email.ca,"123 Main Street, City, Province",National Microbiology Laboratory (NML),RespLab@lab.ca,"123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada",2018-03-01,,30-Apr,Canda,BC,Thunder Bay,Severe acute respiratory syndrome coronavirus 2,hCov-19/CANADA/BC-prov_rona_99/2020,Surveillance testing,Not Provided,Not Applicable,  Reinfection testing,Not Applicable,Lungs,Not Applicable,Not Applicable,Not Applicable,Swab,Not Applicable,SOP123,Not Provided,Not Provided,Not Applicable,Not Applicable,Not Applicable,Not Provided,Batman,Homo chiroptera,Sick,  Hospitalized (ICU),Recovered,,89,,80 - 89,Female,Cnada,British Columbia,PHN1234,2022-02-23,Cough;Fever,Not Provided,Not Provided,Fully Vaccinated,3,Pfizer-BioNTech (Comirnaty),2021-07-01,Pfizer-BioNTech (Comirnaty),2021-11-02,Moderna (Spikevax),2022-02-01,,,,United States of America,Portland,Oregon,United States of America,2022-03-02,05-2020,Air,day 10,,Occupational exposure (retail),direct human to human,Attendee,"Occupational, Residency or Patronage Exposure",,Prior infection,SARS-CoV-2/human/USA/CA-CDPH-001/2020,2021-06-01,Prior antiviral treatment,remdesivir,2021-06-05,      Surveillance of international border crossing by air travel,Not Provided,,XYZ_123345,1200bp,Nextera XT,FAB06069,  Illumina NextSeq 2000,SeqProt1234,"Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.",1234546,Freed,Trimmomatic 0.38,,ncov123assembly3,ncov123assembly.fasta,User/Documents/RespLab/Data/ncov123assembly.fasta,iVar,1.3,95%,400x,100x,ABC123_S1_L001_R1_001.fastq.gz,ABC123_S1_L001_R2_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz,rona123assembly.fast5,User/Documents/RespLab/Data/rona123assembly.fast5,387566,38677,330,NC_045512.2,https://github.com/phac-nml/ncov2019-artic-nf,B.1.1.7,Pangolin,2.1.10,VOC,Sequencing,"Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L).",E gene (orf4),,21.2,Spike (orf2),,19.2,,,,"Tejinder Singh, Fei Hu, Joe Blogs",DataHarmonizer provenance: v0.15.3
-sample1234,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,DataHarmonizer provenance: v0.15.3
-sample1234,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,DataHarmonizer provenance: v0.15.3
+sample123,Switch Health,abc12345,case4444,NMLsample2222,prov_rona_99,PRJNA623807,PRJNA608651,SAMN14180202,SRR11177792,MN908947.3,EPI_ISL_436489,SharEd hospital Laboratory,switch@email.ca,"123 Main Street, City, Province",National Microbiology Laboratory (NML),RespLab@lab.ca,"123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada",2018-03-01,,30-Apr,Canda,BC,Thunder Bay,Severe acute respiratory syndrome coronavirus 2,hCov-19/CANADA/BC-prov_rona_99/2020,Surveillance testing,Not Provided,Not Applicable,  Reinfection testing,Not Applicable,Lungs,Not Applicable,Not Applicable,Not Applicable,Swab,Not Applicable,SOP123,Not Provided,Not Provided,Not Applicable,Not Applicable,Not Applicable,Not Provided,Batman,Homo chiroptera,Sick,  Hospitalized (ICU),Recovered,,89,,80 - 89,Female,Cnada,British Columbia,PHN1234,2022-02-23,Cough;Fever,Not Provided,Not Provided,Fully Vaccinated,3,Pfizer-BioNTech (Comirnaty),2021-07-01,Pfizer-BioNTech (Comirnaty),2021-11-02,Moderna (Spikevax),2022-02-01,,,,United States of America,Portland,Oregon,United States of America,2022-03-02,05-2020,Air,day 10,,Occupational exposure (retail),direct human to human,Attendee,"Occupational, Residency or Patronage Exposure",,Prior infection,SARS-CoV-2/human/USA/CA-CDPH-001/2020,2021-06-01,Prior antiviral treatment,remdesivir,2021-06-05,      Surveillance of international border crossing by air travel,Not Provided,,XYZ_123345,1200bp,Nextera XT,FAB06069,  Illumina NextSeq 2000,SeqProt1234,"Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.",1234546,Freed,Trimmomatic 0.38,,ncov123assembly3,ncov123assembly.fasta,User/Documents/RespLab/Data/ncov123assembly.fasta,iVar,1.3,95%,400x,100x,ABC123_S1_L001_R1_001.fastq.gz,ABC123_S1_L001_R2_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz,rona123assembly.fast5,User/Documents/RespLab/Data/rona123assembly.fast5,387566,38677,330,NC_045512.2,https://github.com/phac-nml/ncov2019-artic-nf,B.1.1.7,Pangolin,2.1.10,VOC,Sequencing,"Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L).",E gene (orf4),,21.2,Spike (orf2),,19.2,,,,"Tejinder Singh, Fei Hu, Joe Blogs",DataHarmonizer provenance: v0.15.4
+sample1234,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,DataHarmonizer provenance: v0.15.4
+sample1234,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,DataHarmonizer provenance: v0.15.4
diff --git a/template/canada_covid19/exampleInput/validTestData_0-15-4.xlsx b/template/canada_covid19/exampleInput/validTestData_0-15-4.xlsx
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diff --git a/template/canada_covid19/exampleInput/validTestData_0-15-4.csv b/template/canada_covid19/exampleInput/validTestData_0-15-5.csv
similarity index 62%
rename from template/canada_covid19/exampleInput/validTestData_0-15-4.csv
rename to template/canada_covid19/exampleInput/validTestData_0-15-5.csv
index 9f2a2cb6..0e682667 100644
--- a/template/canada_covid19/exampleInput/validTestData_0-15-4.csv
+++ b/template/canada_covid19/exampleInput/validTestData_0-15-5.csv
@@ -1,3 +1,3 @@
 Database Identifiers,,,,,,,,,,,,Sample collection and processing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Host Information,,,,,,,,,,,,,,,,,Host vaccination information,,,,,,,,,,,Host exposure information,,,,,,,,,,,,,,Host reinfection information,,,,,,Sequencing,,,,,,,,,,,,Bioinformatics and QC metrics,,,,,,,,,,,,,,,,,,,,,Lineage and Variant information,,,,,,Pathogen diagnostic testing,,,,,,,,,Contributor acknowledgement,
 specimen collector sample ID,third party lab service provider name,third party lab sample ID,case ID,Related specimen primary ID,IRIDA sample name,umbrella bioproject accession,bioproject accession,biosample accession,SRA accession,GenBank accession,GISAID accession,sample collected by,sample collector contact email,sample collector contact address,sequence submitted by,sequence submitter contact email,sequence submitter contact address,sample collection date,sample collection date precision,sample received date,geo_loc_name (country),geo_loc_name (state/province/territory),geo_loc_name (city),organism,isolate,purpose of sampling,purpose of sampling details,NML submitted specimen type,Related specimen relationship type,anatomical material,anatomical part,body product,environmental material,environmental site,collection device,collection method,collection protocol,specimen processing,specimen processing details,lab host,passage number,passage method,biomaterial extracted,host (common name),host (scientific name),host health state,host health status details,host health outcome,host disease,host age,host age unit,host age bin,host gender,host residence geo_loc name (country),host residence geo_loc name (state/province/territory),host subject ID,symptom onset date,signs and symptoms,pre-existing conditions and risk factors,complications,host vaccination status,number of vaccine doses received,vaccination dose 1 vaccine name,vaccination dose 1 vaccination date,vaccination dose 2 vaccine name,vaccination dose 2 vaccination date,vaccination dose 3 vaccine name,vaccination dose 3 vaccination date,vaccination dose 4 vaccine name,vaccination dose 4 vaccination date,vaccination history,location of exposure geo_loc name (country),destination of most recent travel (city),destination of most recent travel (state/province/territory),destination of most recent travel (country),most recent travel departure date,most recent travel return date,travel point of entry type,border testing test day type,travel history,exposure event,exposure contact level,host role,exposure setting,exposure details,prior SARS-CoV-2 infection,prior SARS-CoV-2 infection isolate,prior SARS-CoV-2 infection date,prior SARS-CoV-2 antiviral treatment,prior SARS-CoV-2 antiviral treatment agent,prior SARS-CoV-2 antiviral treatment date,purpose of sequencing,purpose of sequencing details,sequencing date,library ID,amplicon size,library preparation kit,flow cell barcode,sequencing instrument,sequencing protocol name,sequencing protocol,sequencing kit number,amplicon pcr primer scheme,raw sequence data processing method,dehosting method,consensus sequence name,consensus sequence filename,consensus sequence filepath,consensus sequence software name,consensus sequence software version,breadth of coverage value,depth of coverage value,depth of coverage threshold,r1 fastq filename,r2 fastq filename,r1 fastq filepath,r2 fastq filepath,fast5 filename,fast5 filepath,number of base pairs sequenced,consensus genome length,Ns per 100 kbp,reference genome accession,bioinformatics protocol,lineage/clade name,lineage/clade analysis software name,lineage/clade analysis software version,variant designation,variant evidence,variant evidence details,gene name 1,diagnostic pcr protocol 1,diagnostic pcr Ct value 1,gene name 2,diagnostic pcr protocol 2,diagnostic pcr Ct value 2,gene name 3,diagnostic pcr protocol 3,diagnostic pcr Ct value 3,authors,DataHarmonizer provenance
-sample1234,Switch Health,abc12345,case4444,NMLsample2222,prov_rona_99,PRJNA623807,PRJNA608651,SAMN14180202,SRR11177792,MN908947.3,EPI_ISL_436489,Switch Health,switch@email.ca,"123 Main Street, City, Province",National Microbiology Laboratory (NML),RespLab@lab.ca,"123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada",2022-03-01,day,2022-03-15,Canada,British Columbia,Thunder Bay,Severe acute respiratory syndrome coronavirus 2,hCov-19/CANADA/BC-prov_rona_99/2020,Diagnostic testing,Not Provided,Not Applicable,  Reinfection testing,Not Applicable,Nasopharynx (NP); Oropharynx (OP),Not Applicable,Not Applicable,Not Applicable,Swab,Not Applicable,SOP123,Not Provided,Not Provided,Not Applicable,Not Applicable,Not Applicable,Not Provided,Human,Homo sapiens,Symptomatic,  Hospitalized (ICU),Recovered,COVID-19,34,year,30 - 39,Female,Canada,British Columbia,PHN1234,2022-02-23,Cough;Fever,Not Provided,Not Provided,Fully Vaccinated,3,Pfizer-BioNTech (Comirnaty),2021-07-01,Pfizer-BioNTech (Comirnaty),2021-11-02,Moderna (Spikevax),2022-02-01,,,,United States of America,Portland,Oregon,United States of America,2022-03-02,2022-03-11,Air,day 10,,  Convention,"    Close contact (face-to-face, no direct contact)",Attendee,"Occupational, Residency or Patronage Exposure",,Prior infection,SARS-CoV-2/human/USA/CA-CDPH-001/2020,2021-06-01,Prior antiviral treatment,remdesivir,2021-06-05,      Surveillance of international border crossing by air travel,Not Provided,2022-04-04,XYZ_123345,1200bp,Nextera XT,FAB06069,  Illumina NextSeq 2000,SeqProt1234,"Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.",1234546,Freed,Trimmomatic 0.38,Nanostripper,ncov123assembly3,ncov123assembly.fasta,User/Documents/RespLab/Data/ncov123assembly.fasta,iVar,1.3,95%,400x,100x,ABC123_S1_L001_R1_001.fastq.gz,ABC123_S1_L001_R2_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz,rona123assembly.fast5,User/Documents/RespLab/Data/rona123assembly.fast5,387566,38677,330,NC_045512.2,https://github.com/phac-nml/ncov2019-artic-nf,B.1.1.7,Pangolin,2.1.10,Variant of Concern (VOC),Sequencing,"Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L).",E gene (orf4),,21.2,  RdRp gene (nsp12),,19.2,,,,"Tejinder Singh, Fei Hu, Joe Blogs",DataHarmonizer provenance: v0.15.4
+sample1234,Switch Health,abc12345,case4444,NMLsample2222,prov_rona_99,PRJNA623807,PRJNA608651,SAMN14180202,SRR11177792,MN908947.3,EPI_ISL_436489,Shared Hospital Laboratory,shl@email.ca,"123 Main Street, City, Province",National Microbiology Laboratory (NML),RespLab@lab.ca,"123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada",2022-03-01,day,2022-03-15,Canada,British Columbia,Thunder Bay,Severe acute respiratory syndrome coronavirus 2,hCov-19/CANADA/BC-prov_rona_99/2020,Diagnostic testing,Not Provided,Not Applicable,  Reinfection testing,Not Applicable,  Nasopharynx (NP);  Oropharynx (OP),Not Applicable,Not Applicable,Not Applicable,Swab,Not Applicable,SOP123,Not Provided,Not Provided,Not Applicable,Not Applicable,Not Applicable,Not Provided,Human,Homo sapiens,Symptomatic,  Hospitalized (ICU),Recovered,COVID-19,34,year,30 - 39,Female,Canada,British Columbia,PHN1234,2022-02-23,Cough;Fever,Not Provided,Not Provided,Fully Vaccinated,3,Pfizer-BioNTech (Comirnaty),2021-07-01,Pfizer-BioNTech (Comirnaty),2021-11-02,Moderna (Spikevax),2022-02-01,,,,United States of America,Portland,Oregon,United States of America,2022-03-02,2022-03-11,Air,day 10,,  Convention,"    Close contact (face-to-face, no direct contact)",Attendee,"Occupational, Residency or Patronage Exposure",,Prior infection,SARS-CoV-2/human/USA/CA-CDPH-001/2020,2021-06-01,Prior antiviral treatment,remdesivir,2021-06-05,      Surveillance of international border crossing by air travel,Not Provided,2022-04-04,XYZ_123345,1200bp,Nextera XT,FAB06069,  Illumina NextSeq 2000,SeqProt1234,"Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.",1234546,Freed,Trimmomatic 0.38,Nanostripper,ncov123assembly3,ncov123assembly.fasta,User/Documents/RespLab/Data/ncov123assembly.fasta,iVar,1.3,95%,400x,100x,ABC123_S1_L001_R1_001.fastq.gz,ABC123_S1_L001_R2_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz,/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz,rona123assembly.fast5,User/Documents/RespLab/Data/rona123assembly.fast5,387566,38677,330,NC_045512.2,https://github.com/phac-nml/ncov2019-artic-nf,B.1.1.7,Pangolin,2.1.10,Variant of Concern (VOC),Sequencing,"Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L).",E gene (orf4),,21.2,  RdRp gene (nsp12),,19.2,,,,"Tejinder Singh, Fei Hu, Joe Blogs",DataHarmonizer provenance: v0.15.4
diff --git a/template/canada_covid19/exampleInput/validTestData_0-15-4.tsv b/template/canada_covid19/exampleInput/validTestData_0-15-5.tsv
similarity index 62%
rename from template/canada_covid19/exampleInput/validTestData_0-15-4.tsv
rename to template/canada_covid19/exampleInput/validTestData_0-15-5.tsv
index d622341c..93c63a15 100644
--- a/template/canada_covid19/exampleInput/validTestData_0-15-4.tsv
+++ b/template/canada_covid19/exampleInput/validTestData_0-15-5.tsv
@@ -1,3 +1,3 @@
 Database Identifiers												Sample collection and processing																																Host Information																	Host vaccination information											Host exposure information														Host reinfection information						Sequencing												Bioinformatics and QC metrics																					Lineage and Variant information						Pathogen diagnostic testing									Contributor acknowledgement	
 specimen collector sample ID	third party lab service provider name	third party lab sample ID	case ID	Related specimen primary ID	IRIDA sample name	umbrella bioproject accession	bioproject accession	biosample accession	SRA accession	GenBank accession	GISAID accession	sample collected by	sample collector contact email	sample collector contact address	sequence submitted by	sequence submitter contact email	sequence submitter contact address	sample collection date	sample collection date precision	sample received date	geo_loc_name (country)	geo_loc_name (state/province/territory)	geo_loc_name (city)	organism	isolate	purpose of sampling	purpose of sampling details	NML submitted specimen type	Related specimen relationship type	anatomical material	anatomical part	body product	environmental material	environmental site	collection device	collection method	collection protocol	specimen processing	specimen processing details	lab host	passage number	passage method	biomaterial extracted	host (common name)	host (scientific name)	host health state	host health status details	host health outcome	host disease	host age	host age unit	host age bin	host gender	host residence geo_loc name (country)	host residence geo_loc name (state/province/territory)	host subject ID	symptom onset date	signs and symptoms	pre-existing conditions and risk factors	complications	host vaccination status	number of vaccine doses received	vaccination dose 1 vaccine name	vaccination dose 1 vaccination date	vaccination dose 2 vaccine name	vaccination dose 2 vaccination date	vaccination dose 3 vaccine name	vaccination dose 3 vaccination date	vaccination dose 4 vaccine name	vaccination dose 4 vaccination date	vaccination history	location of exposure geo_loc name (country)	destination of most recent travel (city)	destination of most recent travel (state/province/territory)	destination of most recent travel (country)	most recent travel departure date	most recent travel return date	travel point of entry type	border testing test day type	travel history	exposure event	exposure contact level	host role	exposure setting	exposure details	prior SARS-CoV-2 infection	prior SARS-CoV-2 infection isolate	prior SARS-CoV-2 infection date	prior SARS-CoV-2 antiviral treatment	prior SARS-CoV-2 antiviral treatment agent	prior SARS-CoV-2 antiviral treatment date	purpose of sequencing	purpose of sequencing details	sequencing date	library ID	amplicon size	library preparation kit	flow cell barcode	sequencing instrument	sequencing protocol name	sequencing protocol	sequencing kit number	amplicon pcr primer scheme	raw sequence data processing method	dehosting method	consensus sequence name	consensus sequence filename	consensus sequence filepath	consensus sequence software name	consensus sequence software version	breadth of coverage value	depth of coverage value	depth of coverage threshold	r1 fastq filename	r2 fastq filename	r1 fastq filepath	r2 fastq filepath	fast5 filename	fast5 filepath	number of base pairs sequenced	consensus genome length	Ns per 100 kbp	reference genome accession	bioinformatics protocol	lineage/clade name	lineage/clade analysis software name	lineage/clade analysis software version	variant designation	variant evidence	variant evidence details	gene name 1	diagnostic pcr protocol 1	diagnostic pcr Ct value 1	gene name 2	diagnostic pcr protocol 2	diagnostic pcr Ct value 2	gene name 3	diagnostic pcr protocol 3	diagnostic pcr Ct value 3	authors	DataHarmonizer provenance
-sample1234	Switch Health	abc12345	case4444	NMLsample2222	prov_rona_99	PRJNA623807	PRJNA608651	SAMN14180202	SRR11177792	MN908947.3	EPI_ISL_436489	Switch Health	switch@email.ca	123 Main Street, City, Province	National Microbiology Laboratory (NML)	RespLab@lab.ca	123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada	2022-03-01	day	2022-03-15	Canada	British Columbia	Thunder Bay	Severe acute respiratory syndrome coronavirus 2	hCov-19/CANADA/BC-prov_rona_99/2020	Diagnostic testing	Not Provided	Not Applicable	  Reinfection testing	Not Applicable	Nasopharynx (NP); Oropharynx (OP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable	SOP123	Not Provided	Not Provided	Not Applicable	Not Applicable	Not Applicable	Not Provided	Human	Homo sapiens	Symptomatic	  Hospitalized (ICU)	Recovered	COVID-19	34	year	30 - 39	Female	Canada	British Columbia	PHN1234	2022-02-23	Cough;Fever	Not Provided	Not Provided	Fully Vaccinated	3	Pfizer-BioNTech (Comirnaty)	2021-07-01	Pfizer-BioNTech (Comirnaty)	2021-11-02	Moderna (Spikevax)	2022-02-01				United States of America	Portland	Oregon	United States of America	2022-03-02	2022-03-11	Air	day 10		  Convention	    Close contact (face-to-face, no direct contact)	Attendee	Occupational, Residency or Patronage Exposure		Prior infection	SARS-CoV-2/human/USA/CA-CDPH-001/2020	2021-06-01	Prior antiviral treatment	remdesivir	2021-06-05	      Surveillance of international border crossing by air travel	Not Provided	2022-04-04	XYZ_123345	1200bp	Nextera XT	FAB06069	  Illumina NextSeq 2000	SeqProt1234	Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.	1234546	Freed	Trimmomatic 0.38	Nanostripper	ncov123assembly3	ncov123assembly.fasta	User/Documents/RespLab/Data/ncov123assembly.fasta	iVar	1.3	95%	400x	100x	ABC123_S1_L001_R1_001.fastq.gz	ABC123_S1_L001_R2_001.fastq.gz	/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz	/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz	rona123assembly.fast5	User/Documents/RespLab/Data/rona123assembly.fast5	387566	38677	330	NC_045512.2	https://github.com/phac-nml/ncov2019-artic-nf	B.1.1.7	Pangolin	2.1.10	Variant of Concern (VOC)	Sequencing	Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L).	E gene (orf4)		21.2	  RdRp gene (nsp12)		19.2				Tejinder Singh, Fei Hu, Joe Blogs	DataHarmonizer provenance: v0.15.4
+sample1234	Switch Health	abc12345	case4444	NMLsample2222	prov_rona_99	PRJNA623807	PRJNA608651	SAMN14180202	SRR11177792	MN908947.3	EPI_ISL_436489	Shared Hospital Laboratory	shl@email.ca	123 Main Street, City, Province	National Microbiology Laboratory (NML)	RespLab@lab.ca	123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada	2022-03-01	day	2022-03-15	Canada	British Columbia	Thunder Bay	Severe acute respiratory syndrome coronavirus 2	hCov-19/CANADA/BC-prov_rona_99/2020	Diagnostic testing	Not Provided	Not Applicable	  Reinfection testing	Not Applicable	  Nasopharynx (NP);  Oropharynx (OP)	Not Applicable	Not Applicable	Not Applicable	Swab	Not Applicable	SOP123	Not Provided	Not Provided	Not Applicable	Not Applicable	Not Applicable	Not Provided	Human	Homo sapiens	Symptomatic	  Hospitalized (ICU)	Recovered	COVID-19	34	year	30 - 39	Female	Canada	British Columbia	PHN1234	2022-02-23	Cough;Fever	Not Provided	Not Provided	Fully Vaccinated	3	Pfizer-BioNTech (Comirnaty)	2021-07-01	Pfizer-BioNTech (Comirnaty)	2021-11-02	Moderna (Spikevax)	2022-02-01				United States of America	Portland	Oregon	United States of America	2022-03-02	2022-03-11	Air	day 10		  Convention	    Close contact (face-to-face, no direct contact)	Attendee	Occupational, Residency or Patronage Exposure		Prior infection	SARS-CoV-2/human/USA/CA-CDPH-001/2020	2021-06-01	Prior antiviral treatment	remdesivir	2021-06-05	      Surveillance of international border crossing by air travel	Not Provided	2022-04-04	XYZ_123345	1200bp	Nextera XT	FAB06069	  Illumina NextSeq 2000	SeqProt1234	Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.	1234546	Freed	Trimmomatic 0.38	Nanostripper	ncov123assembly3	ncov123assembly.fasta	User/Documents/RespLab/Data/ncov123assembly.fasta	iVar	1.3	95%	400x	100x	ABC123_S1_L001_R1_001.fastq.gz	ABC123_S1_L001_R2_001.fastq.gz	/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz	/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz	rona123assembly.fast5	User/Documents/RespLab/Data/rona123assembly.fast5	387566	38677	330	NC_045512.2	https://github.com/phac-nml/ncov2019-artic-nf	B.1.1.7	Pangolin	2.1.10	Variant of Concern (VOC)	Sequencing	Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L).	E gene (orf4)		21.2	  RdRp gene (nsp12)		19.2				Tejinder Singh, Fei Hu, Joe Blogs	DataHarmonizer provenance: v0.15.4
diff --git a/template/canada_covid19/exampleInput/validTestData_0-15-4.xls b/template/canada_covid19/exampleInput/validTestData_0-15-5.xls
similarity index 92%
rename from template/canada_covid19/exampleInput/validTestData_0-15-4.xls
rename to template/canada_covid19/exampleInput/validTestData_0-15-5.xls
index e0d864fa8e57741c43bf61470882c4493017853c..8658c7916ec1c4d71a95b7b55dfe78fe2cfb6d9b 100644
GIT binary patch
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diff --git a/template/canada_covid19/exampleInput/validTestData_0-15-5.xlsx b/template/canada_covid19/exampleInput/validTestData_0-15-5.xlsx
new file mode 100644
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