Update logic for no SRR accessions and invalid samples

theiagen · Nov 22, 2024 · e186b30 · e186b30
1 parent 26d8c49
commit e186b30
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diff --git a/docs/workflows/public_data_sharing/fetch_srr_accession.md b/docs/workflows/public_data_sharing/fetch_srr_accession.md
@@ -16,11 +16,11 @@ The workflow uses the fastq-dl tool to fetch metadata from SRA and specifically
 
 | **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 | **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 |
+| 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 |
+| 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 |
 
 ### Workflow Tasks
 
@@ -35,7 +35,7 @@ This workflow has a single task that performs metadata retrieval for the specifi
         | 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 Publication](https://doi.org/10.1186/s12859-021-04346-3) |
+        | Original Publication | [fastq-dl: A fast and reliable tool for downloading SRA metadata](https://doi.org/10.1186/s12859-021-04346-3) |
 
 ### Outputs
 

diff --git a/tasks/utilities/data_handling/task_fetch_srr_accession.wdl b/tasks/utilities/data_handling/task_fetch_srr_accession.wdl
@@ -11,51 +11,39 @@ task fetch_srr_accession {
   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
 
-    # Fetch metadata for the sample accession
-    echo "Fetching metadata for valid biosample ID or SRA: ~{sample_accession}"
-    if fastq-dl --accession ~{sample_accession} --only-download-metadata --verbose 2> stderr; then
-        if [[ -f fastq-run-info.tsv ]]; then
-            echo "Metadata written for valid biosample ID or SRA: ~{sample_accession}"
-            cat fastq-run-info.tsv
+    echo "Fetching metadata for accession: ~{sample_accession}"
 
-            # Extract SRR accessions from the TSV file
-            SRR_accessions=$(awk -F'\t' 'NR>1 {print $1}' fastq-run-info.tsv | paste -sd ',' -)
+    # Run fastq-dl and capture stderr
+    fastq-dl --accession ~{sample_accession} --only-download-metadata -m 2 --verbose 2> stderr.log || true
 
-            if [[ -z "${SRR_accessions}" ]]; then
-                # Valid biosample ID or SRA, but no SRR accessions found
-                echo "No SRR accession found for valid biosample ID or SRA: ~{sample_accession}" > srr_accession.txt
-            else
-                # Valid biosample ID or SRA with SRR accessions
-                echo "Extracted SRR accessions: ${SRR_accessions}"
-                echo "${SRR_accessions}" > srr_accession.txt
-            fi
-        else
-            # No metadata file generated, treat as no SRRs found for valid biosample
-            echo "No metadata file found for valid biosample ID or SRA: ~{sample_accession}"
-            echo "No SRR accession found" > srr_accession.txt
-        fi
+    # 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
-        # Check stderr for specific error messages
-        if grep -q "Query was successful, but received an empty response" stderr; then
-            # Valid biosample ID or SRA, but no data found output No SRR accession found
-            echo "No SRR accession found for valid biosample ID or SRA: ~{sample_accession} -Query was successful, but received an empty response" > srr_accession.txt
+        # 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
-        elif grep -q "is not a Study, Sample, Experiment, or Run accession" stderr; then
-            # Invalid accession ID or SRA Fail workflow
-            echo "Invalid biosample ID or SRA: ~{sample_accession}"
-            exit 1
         else
-            # Unexpected error
-            echo "fastq-dl failed for ~{sample_accession} due to an unknown error."
-            exit 1
+            echo "Extracted SRR accessions: ${SRR_accessions}"
+            echo "${SRR_accessions}" > srr_accession.txt
         fi
     fi
   >>>

diff --git a/workflows/utilities/data_import/wf_fetch_srr_accession.wdl b/workflows/utilities/data_import/wf_fetch_srr_accession.wdl
@@ -3,7 +3,7 @@ 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 {
+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."
   }
@@ -13,14 +13,14 @@ workflow fetch_srr {
   call versioning_task.version_capture {
     input:
   }
-  call srr_task.fetch_srr_accession {
+  call srr_task.fetch_srr_accession as fetch_srr {
     input:
       sample_accession = sample_accession
   }
   output {
-    String srr_accession = fetch_srr_accession.srr_accession
+    String srr_accession = fetch_srr.srr_accession
     # Version Captures
-    String phb_version = version_capture.phb_version
-    String fetch_srr_date = version_capture.date
+    String fetch_srr_accession_version = version_capture.phb_version
+    String fetch_srr_accession_analysis_date = version_capture.date
   }
-}
+}