Add WDL Workflow: Generate summary reports for malaria samples

.dockstore.yml

@@ -96,3 +96,6 @@ workflows:
 - name: CleanupIntermediate
   subclass: wdl
   primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CleanupIntermediate.wdl
+- name: GenerateMalariaReport
+  subclass: wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/MalariaReportsWorkflow.wdl

.gitignore

@@ -10,3 +10,5 @@ venv/
 .tox
 test/test_output/
 __pycache__
+*.zip
+docker/lr-malaria-reports/report-files/Senegal_Terra_Metadata.csv

docker/lr-malaria-reports/.gitignore

@@ -0,0 +1,11 @@
+templates/map.html
+test_data/
+data/
+/.vscode
+*_report.html
+*.jpeg
+*.json
+*.ipynb
+*.txt
+*.bed.gz
+test.html

docker/lr-malaria-reports/Dockerfile

@@ -0,0 +1,36 @@
+# Base image
+FROM continuumio/miniconda3:4.9.2
+
+LABEL Bridget Knight
+
+# install gsutil
+RUN apt-get --allow-releaseinfo-change update
+RUN apt install -y curl git-lfs parallel
+RUN curl https://sdk.cloud.google.com | bash
+
+# Setup crcmodc for gsutil:
+RUN apt-get install -y gcc python3-dev python3-setuptools && \
+			pip3 uninstall -y crcmod && \
+			pip3 install --no-cache-dir -U crcmod
+
+#### Specific for google cloud support
+RUN apt-get install -y gnupg2
+RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list \
+		&& curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg  add - \
+		&& apt-get update -y \
+		&& apt-get install google-cloud-sdk -y
+
+# make sure pip is up to date
+RUN pip3 install --upgrade pip==23.2.1
+
+# install other packages
+RUN pip3 install --no-cache-dir NumPy==1.24.4
+RUN pip3 install --no-cache-dir pandas==1.3.0
+RUN pip3 install --no-cache-dir argparse==1.4.0 folium==0.14.0 jinja2==3.1.2 \
+		MarkupSafe==2.1.3 matplotlib==3.7.3 \
+		plotly==5.15.0 tabulate==0.9.0
+
+ENV PATH=/root/google-cloud-sdk/bin/:${PATH}
+
+# copy other resources
+COPY ./report-files /report-files/

docker/lr-malaria-reports/Makefile

@@ -0,0 +1,18 @@
+IMAGE_NAME = lr-malaria-reports
+VERSION = 0.0.2
+
+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)
+