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move to appropriate type
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sage-wright committed Dec 11, 2024
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2 changes: 1 addition & 1 deletion docs/workflows/public_data_sharing/fetch_srr_accession.md
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| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
|---|---|---|---|---|
| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |
| [Data Import](../../workflows_overview/workflows_type.md/#data-import) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |

## Fetch SRR Accession

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2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_type.md
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| [**Assembly_Fetch**](../workflows/data_import/assembly_fetch.md) | Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly | Any taxa | Sample-level | Yes | v1.3.0 | [Assembly_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Assembly_Fetch_PHB:main?tab=info) |
| [**BaseSpace_Fetch**](../workflows/data_import/basespace_fetch.md)| Import data from BaseSpace into Terra | Any taxa | Sample-level | Yes | v2.0.0 | [BaseSpace_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/BaseSpace_Fetch_PHB:main?tab=info) |
| [**Create_Terra_Table**](../workflows/data_import/create_terra_table.md)| Upload data to Terra and then run this workflow to have the table automatically created | Any taxa | | Yes | v2.2.0 | [Create_Terra_Table_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Create_Terra_Table_PHB:main?tab=info) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
| [**SRA_Fetch**](../workflows/data_import/sra_fetch.md)| Import publicly available reads from SRA using SRR#, ERR# or DRR# | Any taxa | Sample-level | Yes | v2.2.0 | [SRA_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/SRA_Fetch_PHB:main?tab=info) |

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|---|---|---|---|---|---|---|
| [**Cauris_CladeTyper**](../workflows/standalone/cauris_cladetyper.md)| C. auris clade assignment | Mycotics | Sample-level | Yes | v1.0.0 | [Cauris_CladeTyper_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Cauris_CladeTyper_PHB:main?tab=info) |
| [**Concatenate_Illumina_Lanes**](../workflows/standalone/concatenate_illumina_lanes.md)| Concatenate Illumina lanes for a single sample | Any taxa | Sample-level | Yes | v2.3.0 | [Concatenate_Illumina_Lanes_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Illumina_Lanes_PHB:main?tab=info) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
| [**GAMBIT_Query**](../workflows/standalone/gambit_query.md)| Taxon identification of genome assembly using GAMBIT | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [Gambit_Query_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Gambit_Query_PHB:main?tab=info) |
| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.3.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
| [**NCBI-AMRFinderPlus**](../workflows/standalone/ncbi_amrfinderplus.md)| Runs NCBI's AMRFinderPlus on genome assemblies (bacterial and fungal) | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [NCBI-AMRFinderPlus_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI-AMRFinderPlus_PHB:main?tab=info) |
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