changes to dorado basecall task: added logic for selecting model to b…

…e used at runtime; improved logging of dorado STDERR to a file; parsed explict model name from STDERR file or accept user input string; added dorado_log task output file

tasks/basecalling/task_dorado_basecall.wdl

@@ -17,54 +17,66 @@ task basecall {
     # Capture Dorado version and log it
     dorado --version > DORADO_VERSION 2>&1
     echo "Captured Dorado version:" $(cat DORADO_VERSION)
-
-    # Define the model to use, substituting "sup" with the full model name if given
-    resolved_model="~{dorado_model}"
-    if [ "$resolved_model" = "sup" ]; then
-      resolved_model="[email protected]"
+
+    # if user provides fast, hac, or sup, pass those strings to dorado basecaller command
+    if [ "~{dorado_model}" == "fast" ] || [ "~{dorado_model}" == "hac" ] || [ "~{dorado_model}" == "sup" ]; then
+      dorado_model_variable=~{dorado_model}
+      echo "DEBUG: dorado_model_variable is set to: $dorado_model_variable"
+    # if user provides explicit model name, for example "[email protected]", then provide hardcoded path to directory in container filesystem that has the dorado models
+    else
+      dorado_model_variable="/dorado_models/~{dorado_model}"
+      echo "DEBUG: dorado_model_variable is set to: $dorado_model_variable"
     fi
 
-    # Log the resolved model namet
-    echo "Using Dorado model: $resolved_model"
-    echo "$resolved_model" > "DORADO_MODEL"
-
-    # Define a log file path to capture output
-    log_file="dorado_basecall.log"
-
     # Create a unique output directory for each scatter job
     base_name=$(basename "~{input_file}" .pod5)
     sam_output="output/sam_${base_name}/"
     mkdir -p "$sam_output"
 
-    echo "### Starting basecalling for ~{input_file} ###" | tee -a "$log_file"
+    echo "### Starting basecalling for ~{input_file} ###" | tee -a dorado_basecall.log
 
     # Set SAM file path with unique naming based on POD5 basename
     sam_file="$sam_output/${base_name}.sam"
 
-    echo "Processing ~{input_file}, expected output: $sam_file" | tee -a "$log_file"
+    echo "Processing ~{input_file}, expected output: $sam_file" | tee -a dorado_basecall.log
 
     # Run Dorado basecaller and log output
+    # This part "2> >(tee -a log.txt >&2)" is used to redirect STDERR to the screen AND to append the STDERR to log.txt file. 
+    # Useful for troubleshooting in Terra and for parsing for important information.
     dorado basecaller \
-      "~{dorado_model}" \
+      "${dorado_model_variable}" \
       "~{input_file}" \
       --kit-name ~{kit_name} \
       --emit-sam \
       --no-trim \
       --output-dir "$sam_output" \
-      --verbose | tee -a "$log_file" || { echo "ERROR: Dorado basecaller failed for ~{input_file}"; exit 1; }
+      --verbose 2> >(tee -a dorado_basecall.log >&2) || { echo "ERROR: Dorado basecaller failed for ~{input_file}"; exit 1; }
+
+    # Log the resolved model name
+    echo "DEBUG: Parsing model name from dorado log or capturing string from user input..."
+    if [ "~{dorado_model}" == "fast" || "~{dorado_model}" == "hac" || "~{dorado_model}" == "sup" ]; then
+      echo "DEBUG: User provided either fast, hac, or sup as input for dorado_model variable, parsing log for explicit model name now..."
+      grep -m 1 'downloading' dorado_basecall.log | sed -e 's/.*downloading //' -e 's/ with.*//' | tr -d '\n' | tee DORADO_MODEL
+
+    # (else) if user provides explicit model name, just output that string, no parsing involved
+    else
+      echo "~{dorado_model}" | tee DORADO_MODEL
+    fi
 
     # Rename the generated SAM file to the unique name based on input_file
     generated_sam=$(find "$sam_output" -name "*.sam" | head -n 1)
     mv "$generated_sam" "$sam_file"
 
-    echo "Basecalling completed for ~{input_file}. SAM file renamed to: $sam_file" | tee -a "$log_file"
+    echo "Basecalling completed for ~{input_file}. SAM file renamed to: $sam_file" | tee -a "dorado_basecall.log"
   >>>
 
   output {
     Array[File] sam_files = glob("output/sam_*/*.sam")
     String dorado_docker = docker
     String dorado_version = read_string("DORADO_VERSION")
     String dorado_model_used = read_string("DORADO_MODEL")
+    # keeping this dorado_log just for debugging purposes, not a wf output
+    File dorado_log = "dorado_basecall.log"
   }
 
   runtime {