Add Dorado basecalling workflow and update dockstore.yml

.dockstore.yml

@@ -281,5 +281,10 @@ workflows:
  - name: Snippy_Streamline_FASTA_PHB
    subclass: WDL
    primaryDescriptorPath: /workflows/phylogenetics/wf_snippy_streamline_fasta.wdl
+   testParameterFiles:
+    - /tests/inputs/empty.json
+ - name: Dorado_Basecalling_PHB
+   subclass: WDL
+   primaryDescriptorPath: /workflows/utilities/wf_dorado_basecalling.wdl
    testParameterFiles:
     - /tests/inputs/empty.json

workflows/utilities/wf_dorado_basecalling.wdl

@@ -0,0 +1,68 @@
+version 1.0
+
+task dorado_basecall {
+
+  meta {
+    description: "This task performs Dorado basecalling on POD5 files."
+  }
+
+  input {
+    Array[File] input_files
+    String dorado_model
+    String output_prefix
+    String docker = "us-docker.pkg.dev/general-theiagen/staphb/dorado:0.8.0" 
+  }
+
+  command <<< 
+    set -e
+    mkdir -p output 
+
+    # Copy input files 
+    for file in ~{sep=" " input_files}; do 
+      cp "$file" ./ || { echo "Error copying $file" >&2; exit 1; }
+    done 
+
+    # List input files 
+    INPUT_FILES=$(ls *.pod5)
+
+    if [[ -z "$INPUT_FILES" ]]; then
+      echo "No POD5 files found" >&2
+      exit 1
+    fi
+
+    # Run Dorado basecaller using GPU 
+    dorado basecaller \
+      ~{dorado_model} \
+      $INPUT_FILES \
+      --device cuda:all \
+      --emit-fastq \
+      --output-dir output 
+
+    # Rename output 
+    if ls output/*.fastq 1> /dev/null 2>&1; then
+      mv output/*.fastq output/~{output_prefix}.fastq
+    else
+      echo "Error: No FASTQ output generated" >&2
+      exit 1
+    fi
+  >>>
+
+  output {
+    File basecalled_fastq = "output/~{output_prefix}.fastq"
+  }
+
+  runtime {
+    docker: "~{docker}" 
+    cpu: 8
+    memory: "32GB"
+    gpuCount: 1
+  }
+}
+
+# To run this workflow locally, you can still provide a different Docker image:
+# miniwdl run /home/fraser_combe_theiagen_com/workflows/dorado_basecalling.wdl \
+#   input_files=/home/fraser_combe_theiagen_com/workflows/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5 \
+#   dorado_model=/dorado_models/[email protected] \
+#   output_prefix=sample_output \
+#   docker=us-docker.pkg.dev/general-theiagen/staphb/dorado:new_version \
+#   --debug --verbose