doc update dorado workflow

theiagen · Oct 4, 2024 · 9d22c74 · 9d22c74
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diff --git a/docs/workflows/standalone/dorado_basecalling.md b/docs/workflows/standalone/dorado_basecalling.md
@@ -0,0 +1,32 @@
+# Dorado Basecalling Workflow - Version 1.0
+
+## Quick Facts
+
+| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
+|---|---|---|---|---|
+| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | Dorado v1.0 | Yes | Sample-level |
+
+## Dorado Basecalling Overview
+
+The Dorado Basecalling workflow is used to convert Oxford Nanopore `POD5` sequencing files into `FASTQ` format by utilizing a GPU-accelerated environment. This workflow is ideal for high-throughput applications where fast and accurate basecalling is essential.
+
+### Inputs
+
+| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | **Workflow** |
+|---|---|---|---|---|---|---|
+| basecall | **input_files** | Array[File] | Array of `POD5` files to be basecalled | None | Required | Dorado |
+| basecall | **sample_names** | Array[String] | Array of sample names corresponding to the input files | None | Required | Dorado |
+| basecall | **dorado_model** | String | Dorado basecalling model (e.g., `[email protected]`) | None | Required | Dorado |
+| basecall | **output_prefix** | String | Prefix to apply to output files | None | Required | Dorado |
+| basecall | **cpu** | Int | Number of CPUs to allocate to the task | 8 | Optional | Dorado |
+| basecall | **memory** | String | Amount of memory/RAM to allocate to the task | 32GB | Optional | Dorado |
+| basecall | **docker** | String | The Docker container used for this task | us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.0 | Optional | Dorado |
+| basecall | **gpuCount** | Int | Number of GPUs to use for basecalling | 1 | Optional | Dorado |
+| basecall | **gpuType** | String | Type of GPU to use | nvidia-tesla-t4 | Optional | Dorado |
+
+### Outputs
+
+| **Variable** | **Type** | **Description** | **Workflow** |
+|---|---|---|---|
+| basecalled_fastqs | Array[File] | Array of FASTQ files generated from basecalling | Dorado |
+| logs | Array[File] | Array of log files capturing the basecalling process | Dorado |
diff --git a/docs/workflows_overview/workflows_alphabetically.md b/docs/workflows_overview/workflows_alphabetically.md
@@ -16,6 +16,7 @@ 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) |
+| [**Dorado_Basecalling**](../workflows/standalone/dorado_basecalling.md)| GPU-accelerated basecalling of Oxford Nanopore sequencing data | Any taxa | Sample-level | Yes | v1.0.0 | [Dorado_Basecalling_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Dorado_Basecalling_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) |

diff --git a/docs/workflows_overview/workflows_kingdom.md b/docs/workflows_overview/workflows_kingdom.md
@@ -15,6 +15,7 @@ title: Workflows by Kingdom
 | [**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) |
 | [**Concatenate_Column_Content**](../workflows/data_export/concatenate_column_content.md) | Concatenate contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Concatenate_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Column_Content_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) |
+| [**Dorado_Basecalling**](../workflows/standalone/dorado_basecalling.md)| GPU-accelerated basecalling of Oxford Nanopore sequencing data | Any taxa | Sample-level | Yes | v1.0.0 | [Dorado_Basecalling_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Dorado_Basecalling_PHB:main?tab=info) | 
 | [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.0.0 | [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_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
 | [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |

diff --git a/docs/workflows_overview/workflows_type.md b/docs/workflows_overview/workflows_type.md
@@ -71,6 +71,7 @@ title: Workflows by Type
 | **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
 |---|---|---|---|---|---|---|
 | [**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) |
+| [**Dorado_Basecalling**](../workflows/standalone/dorado_basecalling.md)| GPU-accelerated basecalling of Oxford Nanopore sequencing data | Any taxa | Sample-level | Yes | v1.0.0 | [Dorado_Basecalling_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Dorado_Basecalling_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 | v2.0.0 | [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) |

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -52,6 +52,7 @@ nav:
                - Zip_Column_Content: workflows/data_export/zip_column_content.md
             - Standalone:
                - Cauris_CladeTyper: workflows/standalone/cauris_cladetyper.md
+               - Dorado_basecalling: workflows/standalone/dorado_basecalling.md
                - GAMBIT_Query: workflows/standalone/gambit_query.md
                - Kraken2: workflows/standalone/kraken2.md
                - NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
@@ -67,6 +68,7 @@ nav:
                - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md
                - Concatenate_Column_Content: workflows/data_export/concatenate_column_content.md
                - Create_Terra_Table: workflows/data_import/create_terra_table.md
+               - Dorado_basecalling: workflows/standalone/dorado_basecalling.md
                - Kraken2: workflows/standalone/kraken2.md
                - NCBI-Scrub: workflows/standalone/ncbi_scrub.md
                - RASUSA: workflows/standalone/rasusa.md
@@ -126,6 +128,7 @@ nav:
             - Core_Gene_SNP: workflows/phylogenetic_construction/core_gene_snp.md
             - Create_Terra_Table: workflows/data_import/create_terra_table.md
             - CZGenEpi_Prep: workflows/phylogenetic_construction/czgenepi_prep.md
+            - Dorado_basecalling: workflows/standalone/dorado_basecalling.md
             - Find_Shared_Variants: workflows/phylogenetic_construction/find_shared_variants.md
             - Freyja Workflow Series: workflows/genomic_characterization/freyja.md
             - GAMBIT_Query: workflows/standalone/gambit_query.md