diff --git a/docker/lr-dorado/Dockerfile b/docker/lr-dorado/Dockerfile
new file mode 100644
index 000000000..741bac734
--- /dev/null
+++ b/docker/lr-dorado/Dockerfile
@@ -0,0 +1,23 @@
+FROM nvidia/cuda:11.8.0-base-ubuntu22.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && \
+    apt-get install -y wget lsb-release samtools
+
+RUN wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.1-linux-x64.tar.gz && \
+    mkdir -p /opt/ont/dorado/ && \
+    tar zxvf dorado-0.7.1-linux-x64.tar.gz -C /opt/ont/dorado --strip-components=1 && \
+    rm -rf dorado-0.7.1-linux-x64.tar.gz
+
+ENV PATH=/opt/ont/dorado/bin/:${PATH}
+
+RUN apt-get install -yq software-properties-common && \
+    add-apt-repository ppa:deadsnakes/ppa && \
+    apt-get update
+
+RUN apt-get install -yq python3.8 python3.8-distutils curl && \
+    update-alternatives --install /usr/bin/python python /usr/bin/python3.8 2 && \
+    update-alternatives  --set python /usr/bin/python3.8
+
+RUN curl "https://bootstrap.pypa.io/get-pip.py" -o "get-pip.py" && python get-pip.py
+RUN pip install ont-guppy-duplex-pipeline
diff --git a/docker/lr-dorado/Makefile b/docker/lr-dorado/Makefile
new file mode 100644
index 000000000..d243d8fef
--- /dev/null
+++ b/docker/lr-dorado/Makefile
@@ -0,0 +1,17 @@
+IMAGE_NAME = lr-dorado
+VERSION = 0.7.1 # This version number should follow the Guppy version number
+
+TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION)
+TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest
+
+all: | build push
+
+build:
+	docker build -t $(TAG1) -t $(TAG2) .
+
+build_no_cache:
+	docker build --no-cache -t $(TAG1) -t $(TAG2) .
+
+push:
+	docker push $(TAG1)
+	docker push $(TAG2)
diff --git a/wdl/tasks/Preprocessing/Dorado.wdl b/wdl/tasks/Preprocessing/Dorado.wdl
new file mode 100644
index 000000000..05b58026a
--- /dev/null
+++ b/wdl/tasks/Preprocessing/Dorado.wdl
@@ -0,0 +1,410 @@
+version 1.0
+
+##########################################################################################
+# A workflow that runs the Guppy basecaller on ONT FAST5 files.
+# - The docker tag number will match the version of Guppy that is being run. You can change
+#   this value to run a different version of Guppy. Currently supports... [3.5.2, 3.6.0, 4.0.14]
+# - All fast5 files within the given GCS dir, gcs_fast5_dir, will be processed
+# - Takes a few hours to process 130GB. Best guess is that the processing time scales
+#   linearly but untested.
+##########################################################################################
+
+import "Utils.wdl" as Utils
+import "ONTUtils.wdl" as ONT
+import "Structs.wdl"
+
+workflow Dorado {
+
+    meta {
+        description: "Run Guppy basecaller on ONT FAST5 files. The docker tag number will match the version of Guppy that is being run. You can change this value to run a different version of Guppy. Currently supports... [3.5.2, 3.6.0, 4.0.14]. All fast5 files within the given GCS dir, gcs_fast5_dir, will be processed. Takes a few hours to process 130GB. Best guess is that the processing time scales linearly but untested."
+    }
+    parameter_meta {
+        gcs_fast5_dir: "GCS path to a directory containing ONT FAST5 files."
+        config: "Guppy config file."
+        barcode_kit: "Optional. Barcode kit used for sequencing. "
+        instrument: "Optional. Instrument used for sequencing. Default is 'unknown'."
+        flow_cell_id: "Optional. Flow cell ID used for sequencing. Default is 'unknown'."
+        protocol_run_id: "Optional. Protocol run ID used for sequencing. Default is 'unknown'."
+        sample_name: "Optional. Sample name used for sequencing. Default is 'unknown'."
+        num_shards: "Optional. Number of shards to use for parallelization. Default is 1 + ceil(length(read_lines(ListFast5s.manifest))/100)."
+        gcs_out_root_dir: "GCS path to a directory where the output will be written."
+    }
+
+    input {
+        String gcs_fast5_dir
+
+        String config
+        String? barcode_kit
+
+        String instrument = "unknown"
+        String flow_cell_id = "unknown"
+        String? protocol_run_id
+        String? sample_name
+        Int? num_shards
+
+        File? RefFasta
+        File? RefIndex
+        File? RefFastaDict
+        String gcs_out_root_dir
+    }
+
+    call ListFast5s { input: gcs_fast5_dir = gcs_fast5_dir }
+
+    Int ns = 1 + select_first([num_shards, ceil(length(read_lines(ListFast5s.manifest))/100)])
+    call ONT.PartitionManifest as PartitionFast5Manifest { input: manifest = ListFast5s.manifest, N = ns }
+
+    scatter (chunk_index in range(length(PartitionFast5Manifest.manifest_chunks))) {
+        call Basecall {
+            input:
+                fast5_files  = read_lines(PartitionFast5Manifest.manifest_chunks[chunk_index]),
+                config       = config,
+                kit_name  = barcode_kit,
+                index        = chunk_index,
+                ref_fasta    = RefFasta,
+                ref_index    = RefIndex,
+                ref_fasta_dict = RefFastaDict,
+        }
+    }
+
+    call Utils.Timestamp as TimestampStopped { input: dummy_dependencies = Basecall.sequencing_summary }
+
+    call MakeSequencingSummary { input: sequencing_summaries = Basecall.sequencing_summary }
+
+    call MakeFinalSummary {
+        input:
+            instrument      = instrument,
+            flow_cell_id    = flow_cell_id,
+            sample_id       = select_first([sample_name, Basecall.metadata[0]['sampleid']]),
+            protocol_run_id = select_first([protocol_run_id, Basecall.metadata[0]['runid']]),
+            started         = Basecall.metadata[0]['start_time'],
+            stopped         = TimestampStopped.timestamp
+    }
+
+    call Utils.Uniq as UniqueBarcodes { input: strings = flatten(Basecall.barcodes) }
+
+    call FinalizeBasecalls {
+        input:
+            pass_bams          = flatten(Basecall.pass_bams),
+            sequencing_summary = MakeSequencingSummary.sequencing_summary,
+            final_summary      = MakeFinalSummary.final_summary,
+            barcodes           = UniqueBarcodes.unique_strings,
+            outdir             = gcs_out_root_dir
+    }
+
+    output {
+        String gcs_dir = FinalizeBasecalls.gcs_dir
+        Array[String] barcodes = UniqueBarcodes.unique_strings
+    }
+}
+
+task ListFast5s {
+    input {
+        String gcs_fast5_dir
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    String indir = sub(gcs_fast5_dir, "/$", "")
+
+    command <<<
+        gsutil ls "~{indir}/**.fast5" > fast5_files.txt
+        gsutil ls "~{indir}/**.pod5" >> fast5_files.txt
+    >>>
+
+    output {
+        File manifest = "fast5_files.txt"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          1,
+        mem_gb:             1,
+        disk_gb:            1,
+        boot_disk_gb:       10,
+        preemptible_tries:  0,
+        max_retries:        0,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-utils:0.1.8"
+    }
+    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])
+    }
+}
+
+task Basecall {
+    input {
+        Array[File] fast5_files
+        String config = "sup@latest"
+        String? kit_name
+        Int index = 0
+
+        File? ref_fasta
+        File? ref_index
+        File? ref_fasta_dict
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Int disk_size = 7 * ceil(size(fast5_files, "GB"))
+
+    String ref_arg = if defined(ref_fasta) then "--reference " else ""
+    String demux_arg = if defined(kit_name) then "--kit-name "+kit_name else "--no-classify"
+    String bc_kit_arg = if defined(kit_name) then "--kit-name "+kit_name else ""
+    command <<<
+        set -x
+
+        dorado basecaller \
+            -r \
+            -x "cuda:all" \
+            ~{bc_kit_arg} \
+            ~{ref_arg}~{ref_fasta} \
+            ~{config} \
+            /cromwell_root/ > tmp.output.bam
+
+        dorado demux \
+            ~{demux_arg} \
+            --emit-summary \
+            tmp.output.bam \
+            -o ./dorado_output/
+
+        dorado summary tmp.output.bam > ./dorado_output/sequencing_summary.txt
+
+        # Make a list of the barcodes that were seen in the data
+        find dorado_output/ -name '*.bam' -type f | \
+            awk -F"[/.]" '{ print $(NF-1) }' | \
+            sort -n | \
+            uniq | \
+            tee barcodes.txt
+
+        # rename the
+        find dorado_output/ -name '*bam*' -not -path '*fail*' | awk -F"/" '{ a=NF-1; a=$a; b=$NF; gsub(/dorado_output/, "unclassified", a); c=$NF; for (i = NF-1; i > 0; i--) { c=$i"/"c }; system("mv " c " dorado_output/" a ".chunk_~{index}." b); }'
+
+        # Extract the header for the first bam file
+        samtools view -H $(find dorado_output/ -name '*.bam' -type f | head -1) | grep "@RG" > ./rg_header.txt
+        cat ./rg_header.txt
+
+        # Extract relevant metadata (e.g. sample id, run id, etc.) from the bam header
+        runid=$(grep "^@RG" ./rg_header.txt | grep -o "ID:[^[:space:]]*" | cut -d: -f2 | sed 's/_dna.*//g' | uniq)
+        sampleid=$(grep "^@RG" ./rg_header.txt | grep -o "LB:[^[:space:]]*" | cut -d: -f2 | uniq)
+        start_time=$(grep "^@RG" ./rg_header.txt | grep -o "DT:[^[:space:]]*" | cut -d: -f2 | uniq)
+        model_version_id=$(grep "^@RG" ./rg_header.txt | sed -n 's/.*basecall_model=\([^ ]*\).*/\1/p' | uniq)
+
+        # Ensure uniqueness by picking the first value if multiple values are found
+        runid=$(echo "$runid" | head -1)
+        sampleid=$(echo "$sampleid" | he
+        start_time=$(echo "$start_time" | head -1)
+        model_version_id=$(echo "$model_version_id" | head -1)
+
+        echo -e "runid\t$runid\nsampleid\t$sampleid\nstart_time\t$start_time\nmodel_version_id\t$model_version_id" > metadata.txt
+    >>>
+
+    output {
+        Array[File] pass_bams = glob("dorado_output/*.bam")
+        File sequencing_summary = "dorado_output/sequencing_summary.txt"
+        Array[String] barcodes = read_lines("barcodes.txt")
+        Map[String, String] metadata = read_map("metadata.txt")
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          4,
+        mem_gb:             48,
+        disk_gb:            disk_size,
+        boot_disk_gb:       50,
+        preemptible_tries:  1,
+        max_retries:        1,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-dorado:0.7.1"
+    }
+    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])
+        gpuType:                "nvidia-tesla-v100"
+        gpuCount:               1
+        nvidiaDriverVersion:    "418.152.00"
+        zones:                  ["us-central1-c", "us-central1-f", "us-east1-b", "us-east1-c", "us-west1-a", "us-west1-b"]
+        cpuPlatform:            "Intel Haswell"
+    }
+}
+
+task MakeSequencingSummary {
+    input {
+        Array[File] sequencing_summaries
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Int disk_size = 3*ceil(size(sequencing_summaries, "GB"))
+
+    command <<<
+        set -euxo pipefail
+
+        head -1 ~{sequencing_summaries[0]} > sequencing_summary.txt
+
+        while read p; do
+            awk 'NR > 1 { print }' "$p" >> sequencing_summary.txt
+        done <~{write_lines(sequencing_summaries)}
+    >>>
+
+    output {
+        File sequencing_summary = "sequencing_summary.txt"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          1,
+        mem_gb:             1,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  0,
+        max_retries:        0,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-utils:0.1.8"
+    }
+    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])
+    }
+}
+
+task MakeFinalSummary {
+    input {
+        String instrument
+        String sample_id
+        String flow_cell_id
+        String protocol_run_id
+        String started
+        String stopped
+
+        RuntimeAttr? runtime_attr_override
+    }
+
+    Int disk_size = 1
+
+    command <<<
+        set -euxo pipefail
+
+        echo 'instrument=~{instrument}' > final_summary.txt
+        echo 'flow_cell_id=~{flow_cell_id}' >> final_summary.txt
+        echo 'sample_id=~{sample_id}' >> final_summary.txt
+        echo 'protocol_run_id=~{protocol_run_id}' >> final_summary.txt
+        echo 'started=~{started}' >> final_summary.txt
+        echo 'acquisition_stopped=~{stopped}' >> final_summary.txt
+        echo 'processing_stopped=~{stopped}' >> final_summary.txt
+        echo 'basecalling_enabled=1' >> final_summary.txt
+        echo 'sequencing_summary_file=sequencing_summary.txt' >> final_summary.txt
+    >>>
+
+    output {
+        File final_summary = "final_summary.txt"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          1,
+        mem_gb:             1,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  0,
+        max_retries:        0,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-utils:0.1.8"
+    }
+    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])
+    }
+}
+
+task FinalizeBasecalls {
+    input {
+#        Array[String] pass_fastqs
+        Array[String] pass_bams
+        File sequencing_summary
+        File final_summary
+        Array[String] barcodes
+
+        String outdir
+
+        RuntimeAttr? runtime_attr_override
+    }
+    meta {
+        description: "Copies the given file to the specified bucket."
+        # The volatile keyword forces call caching to be turned off, which is
+        # exactly what we want for this task.
+        # For more info see: https://cromwell.readthedocs.io/en/stable/optimizations/VolatileTasks/
+        volatile: true
+    }
+
+    String gcs_output_dir = sub(outdir + "/", "/+$", "")
+
+    command <<<
+        set -euxo pipefail
+
+        PASS_BAMS="~{write_lines(pass_bams)}"
+
+        while read b; do
+            OUT_DIR="~{gcs_output_dir}/$b"
+            PASS_DIR="$OUT_DIR/pass/"
+
+            grep -w $b $PASS_BAMS | gsutil -m cp -I $PASS_DIR
+
+            if [ ~{length(barcodes)} -eq 1 ]; then
+                cp ~{sequencing_summary} sequencing_summary.$b.txt
+                cp ~{final_summary} final_summary.$b.txt
+            else
+                grep -w -e filename -e $b ~{sequencing_summary} > sequencing_summary.$b.txt
+                sed "s/sample_id=/sample_id=$b./" ~{final_summary} > final_summary.$b.txt
+            fi
+
+            gsutil cp sequencing_summary.$b.txt $OUT_DIR/
+            gsutil cp final_summary.$b.txt $OUT_DIR/
+        done <~{write_lines(barcodes)}
+    >>>
+
+    output {
+        String gcs_dir = gcs_output_dir
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          1,
+        mem_gb:             2,
+        disk_gb:            500,
+        boot_disk_gb:       20,
+        preemptible_tries:  0,
+        max_retries:        0,
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-finalize:0.1.2"
+    }
+    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])
+    }
+}