Update SRR metadata workflow and documentation for clarity and accuracy

.dockstore.yml

@@ -195,7 +195,7 @@ workflows:
    primaryDescriptorPath: /workflows/utilities/data_import/wf_terra_2_bq.wdl
    testParameterFiles:
     - /tests/inputs/empty.json
- - name: Update_srr_metadata_PHB
+ - name: Update_SRR_Metadata_PHB
    subclass: WDL
    primaryDescriptorPath: /workflows/utilities/data_import/wf_update_srr_metadata.wdl
    testParameterFiles:

docs/workflows/public_data_sharing/retrieve_srr_metadata.md

@@ -4,19 +4,21 @@
 
 | **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 v2.2.1 | Yes | Sample-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
 
-This workflow retrieves the Sequence Read Archive (SRA) accession (SRR) associated with a given sample accession. It utilizes the `fastq-dl` tool to fetch metadata from SRA and outputs the 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. | N/A | Required |
+| 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 |
 | fetch_srr_metadata | **docker**| String | Docker image for metadata retrieval. | `us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0` | Optional |
 | fetch_srr_metadata | **disk_size** | Int | Disk space in GB allocated for the task. | 10 | Optional |
 | fetch_srr_metadata | **cpu** | Int | Number of CPUs allocated for the task. | 2 | Optional |
@@ -43,7 +45,7 @@ This workflow has a single task that performs metadata retrieval for the specifi
 
 | **Variable** | **Type** | **Description**|
 |---|---|---|
-| srr_accession| String | The SRR accession associated with the sample ID.|
+| srr_accession| String | The SRR accession associated with the input sample accession.|
 
 ## References
 

docs/workflows_overview/workflows_alphabetically.md

@@ -47,6 +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) |
 | [**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

@@ -24,6 +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) |
 | [**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

@@ -75,6 +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) |
 
 </div>
 

tasks/utilities/data_handling/task_fetch_srr_metadata.wdl

@@ -20,22 +20,25 @@ task fetch_srr_metadata {
     echo "Fetching metadata for sample accession: ${sample_accession}"
 
     # Use fastq-dl to fetch metadata only
-    fastq-dl --accession ~{sample_accession} --provider SRA --outdir metadata_output --only-download-metadata --verbose
+    fastq-dl --accession ~{sample_accession} --outdir metadata_output --only-download-metadata --verbose
+
 
     if [[ -f metadata_output/fastq-run-info.tsv ]]; then
       echo "Metadata written for ${sample_accession}:"
       echo "TSV content:"
       cat metadata_output/fastq-run-info.tsv
 
-      # Extract the SRR accession (assuming it's in the first column)
+      # Extract the SRR accession (It is typically in the first column)
       SRR_accessions=$(awk -F'\t' 'NR>1 {print $1}' metadata_output/fastq-run-info.tsv)
-      echo "Extracted SRR accessions: ${SRR_accessions}"
-
-      # Output the SRR accessions as a single string
-      echo "${SRR_accessions}" > metadata_output/srr_accession.txt
+      if [[ -z "${SRR_accessions}" ]]; then
+        echo "No SRR accession found for ${sample_accession}" > metadata_output/srr_accession.txt
+      else
+        echo "Extracted SRR accessions: ${SRR_accessions}"
+        echo "${SRR_accessions}" > metadata_output/srr_accession.txt
+      fi
     else
       echo "No metadata found for ${sample_accession}"
-      exit 1
+      echo "No SRR accession found" > metadata_output/srr_accession.txt
     fi
   >>>
 
@@ -44,8 +47,9 @@ task fetch_srr_metadata {
   }
   runtime {
     docker: docker
-    memory: memory + " GB"
+    memory: "~{memory} GB"
     cpu: cpu
+    disks: "local-disk " + disk_size + " SSD"
     disk: disk_size + " GB"
     preemptible: 1
   }

workflows/utilities/data_import/wf_update_srr_metadata.wdl

@@ -8,7 +8,6 @@ workflow wf_retrieve_srr {
   }
   input {
     String sample_accession  
-    String retrieve_srr_docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0"
   }
 
   call srr_task.fetch_srr_metadata {