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add sample-level to fetch_srr_accession thing
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sage-wright committed Dec 12, 2024
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2 changes: 1 addition & 1 deletion docs/workflows_overview/workflows_alphabetically.md
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Expand Up @@ -19,7 +19,7 @@ title: Alphabetical Workflows
| [**Core_Gene_SNP**](../workflows/phylogenetic_construction/core_gene_snp.md) | Pangenome analysis | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Core_Gene_SNP_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Core_Gene_SNP_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) |
| [**CZGenEpi_Prep**](../workflows/phylogenetic_construction/czgenepi_prep.md)| Prepare metadata and fasta files for easy upload to the CZ GEN EPI platform. | Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v1.3.0 | [CZGenEpi_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/CZGenEpi_Prep_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) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | Sample-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) |
| [**Find_Shared_Variants**](../workflows/phylogenetic_construction/find_shared_variants.md)| Combines and reshapes variant data from Snippy_Variants to illustrate variants shared across multiple samples | Bacteria, Mycotics | Set-level | Yes | v2.0.0 | [Find_Shared_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Find_Shared_Variants_PHB:main?tab=info) |
| [**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md)| Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.2.0 | [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info), [Freyja_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Update_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) |
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