[Retrieve_SRR_Metadata] New wf to retrieve SRR after Terra2NCBI wf

.dockstore.yml

@@ -195,6 +195,11 @@ workflows:
    primaryDescriptorPath: /workflows/utilities/data_import/wf_terra_2_bq.wdl
    testParameterFiles:
     - /tests/inputs/empty.json
+ - name: Fetch_SRR_Accession_PHB
+   subclass: WDL
+   primaryDescriptorPath: /workflows/utilities/data_import/wf_fetch_srr_accession.wdl
+   testParameterFiles:
+    - /tests/inputs/empty.json
  - name: Concatenate_Column_Content_PHB
    subclass: WDL
    primaryDescriptorPath: /workflows/utilities/file_handling/wf_concatenate_column.wdl

docs/workflows/public_data_sharing/fetch_srr_accession.md

@@ -0,0 +1,52 @@
+# 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 |
+
+## Fetch SRR Accession
+
+This workflow retrieves 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
+
+| **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 |
+| fetch_srr_metadata | **cpu** | Int | Number of CPUs allocated for the task. | 2 | Optional |
+| fetch_srr_metadata | **disk_size** | Int | Disk space in GB allocated for the task. | 10 | Optional |
+| 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 | **memory** | Int | Memory in GB allocated for the task. | 8 | Optional |
+| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
+| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+### 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"
+    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 | 
+        | --- | --- | 
+        | Task | [Task on GitHub](https://github.com/theiagen-org/phb-workflows/blob/main/tasks/utilities/data_handling/task_fetch_srr_metadata.wdl) |
+        | Software Source Code | [fastq-dl Source](https://github.com/rvalieris/fastq-dl) |
+        | Software Documentation | [fastq-dl Documentation](https://github.com/rvalieris/fastq-dl#documentation) |
+        | Original Publication | [fastq-dl: A fast and reliable tool for downloading SRA metadata](https://doi.org/10.1186/s12859-021-04346-3) |
+
+### Outputs
+
+| **Variable** | **Type** | **Description**|
+|---|---|---|
+| srr_accession| String | The SRR accession's associated with the input sample accession.|
+| fetch_srr_accession_version | String | The version of the fetch_srr_accession workflow. |
+| fetch_srr_accession_analysis_date | String | The date the fetch_srr_accession analysis was run. |
+
+## References
+
+> Valieris, R. et al., "fastq-dl: A fast and reliable tool for downloading SRA metadata." Bioinformatics, 2021.

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) |
+| [**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) |
 

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) |
+| [**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) |
 
 </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) |
+| [**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) |
 
 </div>
 

mkdocs.yml

@@ -43,6 +43,7 @@ nav:
                - Samples_to_Ref_Tree: workflows/phylogenetic_placement/samples_to_ref_tree.md
                - Usher_PHB: workflows/phylogenetic_placement/usher.md
             - Public Data Sharing:
+               - Fetch_SRR_Accession: workflows/public_data_sharing/fetch_srr_accession.md
                - Mercury_Prep_N_Batch: workflows/public_data_sharing/mercury_prep_n_batch.md
                - Terra_2_GISAID: workflows/public_data_sharing/terra_2_gisaid.md
                - Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md

tasks/utilities/data_handling/task_fetch_srr_accession.wdl

@@ -0,0 +1,62 @@
+version 1.0
+
+task fetch_srr_accession {
+  input {
+    String sample_accession 
+    String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0"
+    Int disk_size = 10
+    Int cpu = 2
+    Int memory = 8
+  }
+  meta {
+    volatile: true
+  }
+  command <<< 
+    set -euo pipefail
+
+    # Output the current date and fastq-dl version for debugging
+    date -u | tee DATE
+    fastq-dl --version | tee VERSION
+
+    echo "Fetching metadata for accession: ~{sample_accession}"
+
+    # Run fastq-dl and capture stderr
+    fastq-dl --accession ~{sample_accession} --only-download-metadata -m 2 --verbose 2> stderr.log || true
+
+    # Handle whether the ID/accession is valid and contains SRR metadata based on stderr
+    if grep -q "No results found for" stderr.log; then
+        echo "No SRR accession found" > srr_accession.txt
+        echo "No SRR accession found for accession: ~{sample_accession}"
+    elif grep -q "received an empty response" stderr.log; then
+        echo "No SRR accession found" > srr_accession.txt
+        echo "No SRR accession found for accession: ~{sample_accession}"
+    elif grep -q "is not a Study, Sample, Experiment, or Run accession" stderr.log; then
+        echo "Invalid accession: ~{sample_accession}" >&2
+        exit 1
+    elif [[ ! -f fastq-run-info.tsv ]]; then
+        echo "No metadata file found for accession: ~{sample_accession}" >&2
+        exit 1
+    else
+        # Extract SRR accessions from the TSV file if it exists
+        SRR_accessions=$(awk -F'\t' 'NR>1 {print $1}' fastq-run-info.tsv | paste -sd ',' -)
+        if [[ -z "${SRR_accessions}" ]]; then
+            echo "No SRR accession found" > srr_accession.txt
+        else
+            echo "Extracted SRR accessions: ${SRR_accessions}"
+            echo "${SRR_accessions}" > srr_accession.txt
+        fi
+    fi
+  >>>
+  output {
+    String srr_accession = read_string("srr_accession.txt")
+    String fastq_dl_version = read_string("VERSION")
+  }
+  runtime {
+    docker: docker
+    memory: "~{memory} GB"
+    cpu: cpu
+    disks: "local-disk " + disk_size + " SSD"
+    disk: disk_size + " GB"
+    preemptible: 1
+  }
+}

workflows/utilities/data_import/wf_fetch_srr_accession.wdl

@@ -0,0 +1,26 @@
+version 1.0
+
+import "../../../tasks/utilities/data_handling/task_fetch_srr_accession.wdl" as srr_task
+import "../../../tasks/task_versioning.wdl" as versioning_task
+
+workflow fetch_srr_accession {
+  meta {
+    description: "This workflow retrieves the Sequence Read Archive (SRA) accession (SRR) associated with a given sample accession. It uses the fastq-dl tool to fetch metadata from SRA and outputs the SRR accession."
+  }
+  input {
+    String sample_accession  
+  }
+  call versioning_task.version_capture {
+    input:
+  }
+  call srr_task.fetch_srr_accession as fetch_srr {
+    input:
+      sample_accession = sample_accession
+  }
+  output {
+    String srr_accession = fetch_srr.srr_accession
+    # Version Captures
+    String fetch_srr_accession_version = version_capture.phb_version
+    String fetch_srr_accession_analysis_date = version_capture.date
+  }
+}