enhance error handling and logging for biosample ID or SRA fetching

tasks/utilities/data_handling/task_fetch_srr_accession.wdl

@@ -12,7 +12,7 @@ task fetch_srr_accession {
     volatile: true
   }
 
-    command <<< 
+  command <<< 
     set -euo pipefail
 
     # Output the current date and fastq-dl version for debugging
@@ -21,7 +21,7 @@ task fetch_srr_accession {
 
     # 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; then
+    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
@@ -30,22 +30,31 @@ task fetch_srr_accession {
             SRR_accessions=$(awk -F'\t' 'NR>1 {print $1}' fastq-run-info.tsv | paste -sd ',' -)
 
             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
     else
-        # Handle cases where fastq-dl exits with an error
-        if grep -q "No results found" stderr || [[ ! -f fastq-run-info.tsv ]]; then
-            echo "No SRR accession found for valid biosample ID or SRA: ~{sample_accession}"
+        # 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
             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
-            echo "fastq-dl failed for ~{sample_accession}, invalid biosample ID or SRA"
+            # Unexpected error
+            echo "fastq-dl failed for ~{sample_accession} due to an unknown error."
             exit 1
         fi
     fi