Add BarcodeExtractor workflow to extract the barcodes from each inut_bam

wdl/pipelines/TechAgnostic/Utility/BarcodeExtractor.wdl

@@ -0,0 +1,84 @@
+version 1.0
+
+struct RuntimeAttr {
+    Int cpu_cores
+    Int mem_gb
+    Int disk_gb
+    Int boot_disk_gb
+    Int preemptible_tries
+    Int max_retries
+    String docker
+}
+
+workflow BarcodeExtractor {
+    meta {
+        description: "Extract barcode from BAM file and create movie_name.barcode for each sample."
+    }
+    input {
+        File input_file
+        String id
+        String movie_name
+    }
+
+    call ExtractBarcode {
+        input: input_bam_path = input_file
+    }
+
+    output {
+        String barcode = ExtractBarcode.barcode
+        String movie_name_barcode = movie_name + "." + ExtractBarcode.barcode
+    }
+}
+
+task ExtractBarcode {
+    input {
+        String input_bam_path
+        RuntimeAttr? runtime_attr_override
+    }
+
+    command <<<
+    python3 <<CODE
+import re
+import os
+
+def extract_barcode(input_bam):
+    # Extract the filename if the input is a full path
+    filename = os.path.basename(input_bam)
+    match = re.search(r'\\.hifi_reads\\.(bc\\d+)\\.bam', filename)
+    return match.group(1) if match else None
+
+input_bam_path = "${input_bam_path}"
+barcode = extract_barcode(input_bam_path)
+if barcode:
+    print(barcode)
+else:
+    print("No barcode found", file=sys.stderr)
+CODE
+    >>>
+
+    output {
+        String barcode = read_string(stdout())
+    }
+
+    RuntimeAttr default_attr = object {
+        cpu_cores:          2,
+        mem_gb:             8,
+        disk_gb:            50,
+        boot_disk_gb:       10,
+        preemptible_tries:  3,
+        max_retries:        0,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-compile-sv-stats:0.0.0"
+    }
+
+    RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
+
+    runtime {
+        cpu:                    select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
+        memory:                 select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
+        disks:                  "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
+        bootDiskSizeGb:         select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
+        preemptible:            select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
+        maxRetries:             select_first([runtime_attr.max_retries, default_attr.max_retries])
+        docker:                 select_first([runtime_attr.docker, default_attr.docker])
+    }
+}