initial updates

docs/workflows/public_data_sharing/retrieve_srr_metadata.md → docs/workflows/public_data_sharing/fetch_srr_accession.md

@@ -1,21 +1,19 @@
-# Retrieve SRR Metadata Workflow
+# Fetch SRR Accession Workflow
 
 ## Quick Facts
 
 | **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 |
 
-## Retrieve SRR Metadata
+## Fetch SRR Accession
 
 This workflow is designed to retrieve the Sequence Read Archive (SRA) accession (SRR) associated with a given sample accession. The primary inputs are BioSample IDs (e.g., SAMN00000000) or SRA Experiment IDs (e.g., SRX000000), which link to sequencing data in the SRA repository.
 
 The workflow uses the fastq-dl tool to fetch metadata from SRA and specifically parses this metadata to extract the associated SRR accession and outputs the SRR accession.
 
 ### Inputs
 
-<div class="searchable-table" markdown="1">
-
 | **Terra Task Name** | **Variable** | **Type** | **Description**| **Default Value** | **Terra Status** |
 | --- | --- | --- | --- | --- | --- |
 | fetch_srr_metadata | **sample_accession** | String |  SRA-compatible accession, such as a **BioSample ID** (e.g., "SAMN00000000") or **SRA Experiment ID** (e.g., "SRX000000"), used to retrieve SRR metadata. | | Required |
@@ -24,14 +22,12 @@ The workflow uses the fastq-dl tool to fetch metadata from SRA and specifically
 | fetch_srr_metadata | **cpu** | Int | Number of CPUs allocated for the task. | 2 | Optional |
 | fetch_srr_metadata | **memory** | Int | Memory in GB allocated for the task. | 8 | Optional |
 
-</div>
-
 ### Workflow Tasks
 
 This workflow has a single task that performs metadata retrieval for the specified sample accession.
 
 ??? task "`fastq-dl`: Fetches SRR metadata for sample accession"
-    Fetches metadata for a given sample accession using the `fastq-dl` tool. This task uses a Docker container and retrieves the SRR accession by parsing the metadata output.
+    When provided a BioSample accession or SRA experiment ID, 'fastq-dl' collects metadata and returns the appropriate SRR accession.
 
     !!! techdetails "fastq-dl Technical Details"
         |  | Links | 

docs/workflows_overview/workflows_alphabetically.md

@@ -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) |
-| [**Update_SRR_Metadata**](../workflows/public_data_sharing/update_srr_metadata.md)| Update SRR metadata in a Terra data table | Any taxa | | Yes | v2.3.0 | [Update_SRR_Metadata_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Update_SRR_Metadata_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) |
 | [**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) |
 

docs/workflows_overview/workflows_kingdom.md

@@ -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) |
-| [**Update_SRR_Metadata**](../workflows/data_import/update_srr_metadata.md)| Update SRR metadata in a Terra data table | Any taxa | Set-level | Yes | v2.1.0 | [Update_SRR_Metadata_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Update_SRR_Metadata_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) |
 | [**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) |
 
 </div>

docs/workflows_overview/workflows_type.md

@@ -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) |
-| [**Update_SRR_Metadata**](../workflows/public_data_sharing/update_srr_metadata.md)| Update SRR metadata in a Terra data table | Any taxa | | Yes | v2.3.0 | [Update_SRR_Metadata_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Update_SRR_Metadata_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) |
 
 </div>
 

tasks/utilities/data_handling/task_fetch_srr_metadata.wdl → tasks/utilities/data_handling/task_fetch_srr_accession.wdl

@@ -1,6 +1,6 @@
 version 1.0
 
-task fetch_srr_metadata {
+task fetch_srr_accession {
   input {
     String sample_accession 
     String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0"
@@ -41,7 +41,6 @@ task fetch_srr_metadata {
       echo "No SRR accession found" > metadata_output/srr_accession.txt
     fi
   >>>
-
   output {
     String srr_accession = read_string("metadata_output/srr_accession.txt")
   }

workflows/utilities/data_import/wf_update_srr_metadata.wdl → workflows/utilities/data_import/wf_fetch_srr_accession.wdl

@@ -1,6 +1,6 @@
 version 1.0
 
-import "../../../tasks/utilities/data_handling/task_fetch_srr_metadata.wdl" as srr_task
+import "../../../tasks/utilities/data_handling/fetch_srr_accession.wdl" as srr_task
 
 workflow wf_retrieve_srr {
   meta {
@@ -9,12 +9,10 @@ workflow wf_retrieve_srr {
   input {
     String sample_accession  
   }
-
   call srr_task.fetch_srr_metadata {
     input:
       sample_accession = sample_accession
   }
-
   output {
     String srr_accession = fetch_srr_metadata.srr_accession 
   }