Adding a WDL to run DORADO for basecalling ONT data

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

docker/lr-dorado/Makefile

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+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)