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Task/enum update (#174)
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* added IDAT to ResearchDataFileFormatEnum

* updated FlowCellTypeEnums

* updated LibraryPreparationKitRetailNameEnum

* generated artifacts

* addressed comment; updated artifacts
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@mauerk
mauerk authored Dec 17, 2024
1 parent eed3bd1 commit 70e56b8
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13 changes: 13 additions & 0 deletions docs/schema_markdown/FlowCellTypeEnum.md
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Expand Up @@ -16,8 +16,21 @@ URI: [GHGA:FlowCellTypeEnum](https://w3id.org/GHGA/FlowCellTypeEnum)

| Text | Description | Meaning | Other Information |
| :--- | :---: | :---: | ---: |
| ELEMENT_BIOSCIENCES_AVITI_LOW_OUTPUT | Usage of Element Biosciences Aviti Low Output flow cell. | | |
| ELEMENT_BIOSCIENCES_AVITI_MID_OUTPUT | Usage of Element Biosciences Aviti Mid Output flow cell. | | |
| ELEMENT_BIOSCIENCES_AVITI_HIGH_OUTPUT | Usage of Element Biosciences Aviti High Output flow cell. | | |
| ILLUMINA_NOVA_SEQ_SP | Usage of Illumina NovaSeq SP flow cell. | | |
| ILLUMINA_NOVA_SEQ_S1 | Usage of Illumina NovaSeq S1 flow cell. | | |
| ILLUMINA_NOVA_SEQ_S2 | Usage of Illumina NovaSeq S2 flow cell. | | |
| ILLUMINA_NOVA_SEQ_S4 | Usage of Illumina NovaSeq S4 flow cell. | | |
| ILLUMINA_NOVA_SEQ_XPLUS_1_5B | Usage of Illumina NovaSeq X Plus 1.5B flow cell. | | |
| ILLUMINA_NOVA_SEQ_XPLUS_10B | Usage of Illumina NovaSeq X Plus 10B flow cell. | | |
| ILLUMINA_NOVA_SEQ_XPLUS_25B | Usage of Illumina NovaSeq X Plus 25B flow cell. | | |
| ILLUMINA_MISEQ_MICRO | Usage of Illumina MiSeq Micro flow cell. | | |
| ILLUMINA_MISEQ_NANO | Usage of Illumina MiSeq Nano flow cell. | | |
| ILLUMINA_NEXTSEQ_HIGH_OUTPUT | Usage of Illumina NextSeq High Output flow cell. | | |
| ILLUMINA_NEXTSEQ_MID_OUTPUT | Usage of Illumina NextSeq Mid Output flow cell. | | |
| PACBIO_SEQUELL_II | Usage of PacBio Sequell II flow cell. | | |
| PROMETHION | Usage of PromethION flow cell. | | |
| FLONGLE | Usage of Flongle flow cell. | | |
| MINION | Usage of MinION flow cell. | | |
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7 changes: 7 additions & 0 deletions docs/schema_markdown/LibraryPreparationKitRetailNameEnum.md
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Expand Up @@ -18,6 +18,13 @@ URI: [GHGA:LibraryPreparationKitRetailNameEnum](https://w3id.org/GHGA/LibraryPre
| :--- | :---: | :---: | ---: |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V2 | 10X Genomics Chromium Single Cell 3' v2 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V3 | 10X Genomics Chromium Single Cell 3' v3 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V4 | 10X Genomics Chromium Single Cell 3' v4 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_5_V3 | 10X Genomics Chromium Single Cell 5' v3 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_ATAC_V2 | 10X Genomics Chromium ATAC v2 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_MULTIOME_ATAC_RNA | 10X Genomics Chromium Multiome ATAC + RNA Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_VISIUM_FF | 10X Genomics Chromium Visium FF Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_VISIUM_FFPE | 10X Genomics Chromium Visium FFPE Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_VISIUM_CYTASSIST | 10X Genomics Chromium Visium Cytassist Reagent Kit | | |
| ACCEL_NGS_2_S_PLUS_DNA_LIBRARY_KIT | Accel-NGS 2S Plus DNA Library Kit | | |
| ACCEL_NGS_METHYL_SEQ_DNA | Accel-NGS Methyl-Seq DNA Library Kit | | |
| AGILENT_STRAND_SPECIFIC_RNA | Agilent SureSelect Strand Specific RNA Library Preparation Kit | | |
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1 change: 1 addition & 0 deletions docs/schema_markdown/ResearchDataFileFormatEnum.md
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Expand Up @@ -24,5 +24,6 @@ URI: [GHGA:ResearchDataFileFormatEnum](https://w3id.org/GHGA/ResearchDataFileFor
| D | Raw .d files for mass spectrometry proteomics data. | | |
| MZML | mzML format for mass spectrometry proteomics data. | | |
| MZDATA | mzData for mass spectrometry proteomics data. | | |
| IDAT | IDAT file format for BeadArray data. | | |
| OTHER | A file format not captured by the controlled vocabulary. | | |

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63 changes: 63 additions & 0 deletions src/schema/submission.yaml
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Expand Up @@ -1790,6 +1790,9 @@ enums:
MZDATA:
description: >-
mzData for mass spectrometry proteomics data.
IDAT:
description: >-
IDAT file format for BeadArray data.
OTHER:
description: >-
A file format not captured by the controlled vocabulary.
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10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V3:
description: >-
10X Genomics Chromium Single Cell 3' v3 Reagent Kit
10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V4:
description: >-
10X Genomics Chromium Single Cell 3' v4 Reagent Kit
10X_GENOMICS_CHROMIUM_SINGLE_CELL_5_V3:
description: >-
10X Genomics Chromium Single Cell 5' v3 Reagent Kit
10X_GENOMICS_CHROMIUM_ATAC_V2:
description: >-
10X Genomics Chromium ATAC v2 Reagent Kit
10X_GENOMICS_CHROMIUM_MULTIOME_ATAC_RNA:
description: >-
10X Genomics Chromium Multiome ATAC + RNA Reagent Kit
10X_GENOMICS_CHROMIUM_VISIUM_FF:
description: >-
10X Genomics Chromium Visium FF Reagent Kit
10X_GENOMICS_CHROMIUM_VISIUM_FFPE:
description: >-
10X Genomics Chromium Visium FFPE Reagent Kit
10X_GENOMICS_CHROMIUM_VISIUM_CYTASSIST:
description: >-
10X Genomics Chromium Visium Cytassist Reagent Kit
ACCEL_NGS_2_S_PLUS_DNA_LIBRARY_KIT:
description: >-
Accel-NGS 2S Plus DNA Library Kit
Expand Down Expand Up @@ -2771,12 +2795,51 @@ enums:
description: >-
Permitted values for flow cell type.
permissible_values:
ELEMENT_BIOSCIENCES_AVITI_LOW_OUTPUT:
description: >-
Usage of Element Biosciences Aviti Low Output flow cell.
ELEMENT_BIOSCIENCES_AVITI_MID_OUTPUT:
description: >-
Usage of Element Biosciences Aviti Mid Output flow cell.
ELEMENT_BIOSCIENCES_AVITI_HIGH_OUTPUT:
description: >-
Usage of Element Biosciences Aviti High Output flow cell.
ILLUMINA_NOVA_SEQ_SP:
description: >-
Usage of Illumina NovaSeq SP flow cell.
ILLUMINA_NOVA_SEQ_S1:
description: >-
Usage of Illumina NovaSeq S1 flow cell.
ILLUMINA_NOVA_SEQ_S2:
description: >-
Usage of Illumina NovaSeq S2 flow cell.
ILLUMINA_NOVA_SEQ_S4:
description: >-
Usage of Illumina NovaSeq S4 flow cell.
ILLUMINA_NOVA_SEQ_XPLUS_1_5B:
description: >-
Usage of Illumina NovaSeq X Plus 1.5B flow cell.
ILLUMINA_NOVA_SEQ_XPLUS_10B:
description: >-
Usage of Illumina NovaSeq X Plus 10B flow cell.
ILLUMINA_NOVA_SEQ_XPLUS_25B:
description: >-
Usage of Illumina NovaSeq X Plus 25B flow cell.
ILLUMINA_MISEQ_MICRO:
description: >-
Usage of Illumina MiSeq Micro flow cell.
ILLUMINA_MISEQ_NANO:
description: >-
Usage of Illumina MiSeq Nano flow cell.
ILLUMINA_NEXTSEQ_HIGH_OUTPUT:
description: >-
Usage of Illumina NextSeq High Output flow cell.
ILLUMINA_NEXTSEQ_MID_OUTPUT:
description: >-
Usage of Illumina NextSeq Mid Output flow cell.
PACBIO_SEQUELL_II:
description: >-
Usage of PacBio Sequell II flow cell.
PROMETHION:
description: >-
Usage of PromethION flow cell.
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