update workflow remove ouput prefix and run array through dorado

tasks/basecalling/task_dorado_basecall.wdl

@@ -4,7 +4,6 @@ task basecall {
   input {
     Array[File] input_files
     String dorado_model
-    String output_prefix
     String docker = "us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.0"
   }
 
@@ -20,50 +19,23 @@ task basecall {
     echo "Input files: ${input_files_array[@]}"
     echo "Dorado model: ~{dorado_model}"
 
-    # Loop over each input file
-    for file in ${input_files_array[@]}; do
-      base_name=$(basename $file .pod5)
-
-      # Extract barcode (assuming 'barcodeXX' is part of the base name)
-      barcode=$(echo $base_name | grep -o 'barcode[0-9]\+')
-
-      # Create a directory for the current barcode inside the fastq folder
-      barcode_dir="${output_base}${barcode}"
-      mkdir -p ${barcode_dir}/fastqs
-      mkdir -p ${barcode_dir}/logs
-
-      echo "Processing file $file with base name $base_name"
-
-      # Run Dorado basecaller and store outputs in the barcode-specific directories
-      dorado basecaller \
-        /dorado_models/~{dorado_model} \
-        "$file" \
-        --device cuda:all \
-        --emit-fastq \
-        --output-dir ${barcode_dir}/fastqs > ${barcode_dir}/logs/${base_name}_basecaller.log 2>&1 || { echo "Dorado basecaller failed for $file" >&2; exit 1; }
-
-      # Rename each FASTQ file with base name and an index
-      generated_fastqs=(${barcode_dir}/fastqs/*.fastq)
-      if [[ ${#generated_fastqs[@]} -gt 0 ]]; then
-        for idx in ${!generated_fastqs[@]}; do
-          mv "${generated_fastqs[$idx]}" "${barcode_dir}/fastqs/basecalled_${base_name}_part${idx}.fastq"
-        done
-        echo "FASTQ files generated for $base_name"
-      else
-        echo "Error: No FASTQ generated for $file" >&2
-        exit 1
-      fi
-    done
+    # Run Dorado basecaller on all input files
+    dorado basecaller \
+      /dorado_models/~{dorado_model} \
+      ${input_files_array[@]} \
+      --device cuda:all \
+      --emit-fastq \
+      --output-dir ${output_base} > ${output_base}/basecall.log 2>&1 || { echo "Dorado basecaller failed" >&2; exit 1; }
 
     # Log the final directory structure for debugging
     echo "Final output directory structure:"
     ls -lh $output_base
   >>>
 
   output {
-    # Output all the FASTQ files and logs in their respective folders
-    Array[File] basecalled_fastqs = glob("output/fastq/barcode*/fastqs/*.fastq")
-    Array[File] logs = glob("output/fastq/barcode*/logs/*.log")
+    # Output all the FASTQ files and logs in the output folder
+    Array[File] basecalled_fastqs = glob("output/fastq/barcode*/**/*.fastq")
+    Array[File] logs = glob("output/fastq/basecall.log")
   }
 
   runtime {
@@ -75,3 +47,4 @@ task basecall {
     maxRetries: 3
   }
 }
+

workflows/utilities/wf_dorado_basecalling.wdl

@@ -6,14 +6,12 @@ workflow dorado_basecalling_workflow {
   input {
     Array[File] input_files
     String dorado_model
-    String output_prefix
   }
 
   call basecall_task.basecall {
     input:
       input_files = input_files,
-      dorado_model = dorado_model,
-      output_prefix = output_prefix
+      dorado_model = dorado_model
   }
 
   output {