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add sample level to docs
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fraser-combe committed Nov 25, 2024
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2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_alphabetically.md
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Expand Up @@ -47,7 +47,7 @@ title: Alphabetical Workflows
| [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
| [**Transfer_Column_Content**](../workflows/data_export/transfer_column_content.md)| Transfer contents of a specified Terra data table column for many samples ("entities") to a GCP storage bucket location | Any taxa | Set-level | Yes | v1.3.0 | [Transfer_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Transfer_Column_Content_PHB:main?tab=info) |
| [**Samples_to_Ref_Tree**](../workflows/phylogenetic_placement/usher.md)| Use UShER to rapidly and accurately place your samples on any existing phylogenetic tree | Monkeypox virus, SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.1.0 | [Usher_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Usher_PHB:main?tab=info) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table | 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) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table at the sample level | 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) |
| [**Usher_PHB**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v1.2.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
| [**Zip_Column_Content**](../workflows/data_export/zip_column_content.md)| Zip contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Zip_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Zip_Column_Content_PHB:main?tab=info) |

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2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_kingdom.md
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Expand Up @@ -24,7 +24,7 @@ title: Workflows by Kingdom
| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.0.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
| [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
| [**Transfer_Column_Content**](../workflows/data_export/transfer_column_content.md)| Transfer contents of a specified Terra data table column for many samples ("entities") to a GCP storage bucket location | Any taxa | Set-level | Yes | v1.3.0 | [Transfer_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Transfer_Column_Content_PHB:main?tab=info) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table | Any taxa | Set-level | 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) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table at the sample level | Any taxa | Set-level | 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) |
| [**Zip_Column_Content**](../workflows/data_export/zip_column_content.md)| Zip contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Zip_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Zip_Column_Content_PHB:main?tab=info) |

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2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_type.md
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Expand Up @@ -75,7 +75,7 @@ title: Workflows by Type
| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.2.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
| [**Terra_2_GISAID**](../workflows/public_data_sharing/terra_2_gisaid.md)| Upload of assembly data to GISAID | SARS-CoV-2, Viral | Set-level | Yes | v1.2.1 | [Terra_2_GISAID_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_GISAID_PHB:main?tab=info) |
| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table | 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) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Update SRR metadata in a Terra data table at the sample level | 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) |

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