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anna-parkeranna-parker
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Update cchf example (#16)
* feat(cchf): add fastaIds to CCHF metadata entry * wupps * rename submissionId to id
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‎example_files/cchfv_test_metadata.tsv‎

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ampliconPcrPrimerScheme ampliconSize anatomicalMaterial anatomicalPart authorAffiliations authors bodyProduct breadthOfCoverage cellLine collectionDevice collectionMethod consensusSequenceSoftwareName consensusSequenceSoftwareVersion cultureId dehostingMethod depthOfCoverage diagnostic_measurement_method diagnosticMeasurementUnit diagnosticMeasurementValue diagnosticTargetGeneName diagnosticTargetPresence environmentalMaterial environmentalSite experimentalSpecimenRoleType exposureDetails exposureEvent exposureSetting foodProduct foodProductProperties geoLocAdmin1 geoLocAdmin2 geoLocCity geoLocCountry geoLocSite hostAge hostAgeBin hostDisease hostGender hostHealthOutcome hostHealthState hostNameCommon hostNameScientific hostOriginCountry hostRole hostTaxonId hostVaccinationStatus passageMethod passageNumber presamplingActivity previousInfectionDisease previousInfectionOrganism purposeOfSampling purposeOfSequencing qualityControlDetails qualityControlDetermination qualityControlIssues qualityControlMethodName qualityControlMethodVersion rawSequenceDataProcessingMethod referenceGenomeAccession sampleCollectionDate sampleReceivedDate sampleType sequencedByContactEmail sequencedByContactName sequencedByOrganization sequencingAssayType sequencingDate sequencingInstrument sequencingProtocol signsAndSymptoms specimenCollectorSampleId specimenProcessing specimenProcessingDetails bioprojectAccessions submissionId travelHistory versionComment
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"National Institute of Health, Department of Virology" "Ammar, M.; Salman, M.; Umair, M.; Ali, Q.; Hakim, R.; Haider, S.A.; Jamal, Z." Hogwarts Pakistan Homo sapiens 9606 2023-08-26 CCHF/NIHPAK-19/2023 test_NIHPAK-19 "OR964915.1,OR964926.1,OR964937.1"
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fastaIds ampliconPcrPrimerScheme ampliconSize anatomicalMaterial anatomicalPart authorAffiliations authors bodyProduct breadthOfCoverage cellLine collectionDevice collectionMethod consensusSequenceSoftwareName consensusSequenceSoftwareVersion cultureId dehostingMethod depthOfCoverage diagnostic_measurement_method diagnosticMeasurementUnit diagnosticMeasurementValue diagnosticTargetGeneName diagnosticTargetPresence environmentalMaterial environmentalSite experimentalSpecimenRoleType exposureDetails exposureEvent exposureSetting foodProduct foodProductProperties geoLocAdmin1 geoLocAdmin2 geoLocCity geoLocCountry geoLocSite hostAge hostAgeBin hostDisease hostGender hostHealthOutcome hostHealthState hostNameCommon hostNameScientific hostOriginCountry hostRole hostTaxonId hostVaccinationStatus passageMethod passageNumber presamplingActivity previousInfectionDisease previousInfectionOrganism purposeOfSampling purposeOfSequencing qualityControlDetails qualityControlDetermination qualityControlIssues qualityControlMethodName qualityControlMethodVersion rawSequenceDataProcessingMethod referenceGenomeAccession sampleCollectionDate sampleReceivedDate sampleType sequencedByContactEmail sequencedByContactName sequencedByOrganization sequencingAssayType sequencingDate sequencingInstrument sequencingProtocol signsAndSymptoms specimenCollectorSampleId specimenProcessing specimenProcessingDetails bioprojectAccessions id travelHistory versionComment
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test_NIHPAK-19_L test_NIHPAK-19_M test_NIHPAK-19_S "National Institute of Health, Department of Virology" "Ammar, M.; Salman, M.; Umair, M.; Ali, Q.; Hakim, R.; Haider, S.A.; Jamal, Z." Hogwarts Pakistan Homo sapiens 9606 2023-08-26 CCHF/NIHPAK-19/2023 test_NIHPAK-19 "OR964915.1,OR964926.1,OR964937.1"

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