diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js index b3cdc1dc..80f3e9cf 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -61,9 +61,6 @@ var DATA = [ "NML_LIMS": [ { "field": "TEXT_ID" - }, - { - "field": "VD_LAB_NUMBER" } ] } diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index 43d3a0f8..5c23d624 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -2,7 +2,7 @@ Ontology ID parent class label datatype source data status requirement min value ID SC % Database Identifiers Database Identifiers specimen collector sample ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID VD_LAB_NUMBER sample_name - Database Identifiers NML submitted specimen primary ID xs:token The primary ID of the specimen submitted thorough LaSER. Store the identifier for the specimen submitted through the NML LaSER system. SR20-12345 TEXT_ID;VD_LAB_NUMBER + Database Identifiers NML submitted specimen primary ID xs:token The primary ID of the specimen submitted thorough LaSER. Store the identifier for the specimen submitted through the NML LaSER system. SR20-12345 TEXT_ID Database Identifiers NML related specimen primary ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The primary ID of the related specimen previously submitted thorough LaSER Store the primary ID of the related specimen previously submitted thorough LaSER SR20-12345 Related Specimen ID|Related Specimen Relationship Type Database Identifiers IRIDA sample name xs:token The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 Database Identifiers umbrella bioproject accession select UPPER The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 diff --git a/template/canada_covid19/export.js b/template/canada_covid19/export.js index 58041d90..7ffa5f01 100644 --- a/template/canada_covid19/export.js +++ b/template/canada_covid19/export.js @@ -410,6 +410,7 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => { const ExportHeaders = new Map([ ['VD_LAB_NUMBER', []], + ['TEXT_ID', []], ['PH_BIOPROJECT_ACCESSION', []], ['PH_BIOSAMPLE_ACCESSION', []], ['PH_SRA_ACCESSION', []], @@ -444,12 +445,13 @@ var exportNML_LIMS = (baseName, hot, data, xlsx, fileType) => { ['PH_TRAVEL', []], ['PH_EXPOSURE', []], ['PH_TESTING_PROTOCOL', []], - ['RESULT - CANCOGEN_SUBMITTED_RESLT_1', []], - ['RESULT - CANCOGEN_SUBMITTED_RESLT_1CT', []], - ['RESULT - CANCOGEN_SUBMITTED_RESLT_2', []], - ['RESULT - CANCOGEN_SUBMITTED_RESLT_2CT', []], - ['RESULT - CANCOGEN_SUBMITTED_RESLT_3', []], - ['RESULT - CANCOGEN_SUBMITTED_RESLT_3CT', []], + ['SUBMITTED_RESLT - Gene Target #1', []], + ['SUBMITTED_RESLT - Gene Target #1 CT Value', []], + ['SUBMITTED_RESLT - Gene Target #2', []], + ['SUBMITTED_RESLT - Gene Target #2 CT Value', []], + ['SUBMITTED_RESLT - Gene Target #3', []], + ['SUBMITTED_RESLT - Gene Target #3 CT Value', []], + ['PH_CANCOGEN_AUTHORS', []], ['HC_COMMENTS', []] ]);