Merge pull request #369 from lilab-bcb/cumulus-feature-barcoding-docker

Upgrade cumulus_feature_barcoding to v0.11.1 by default

docker/cumulus_feature_barcoding/0.11.1/Dockerfile

@@ -0,0 +1,48 @@
+FROM debian:bullseye-slim
+SHELL ["/bin/bash", "-c"]
+
+ADD https://github.com/lilab-bcb/cumulus_feature_barcoding/archive/refs/tags/0.11.1.tar.gz /software/
+ADD https://raw.githubusercontent.com/lilab-bcb/cumulus/master/docker/monitor_script.sh /software/
+
+RUN apt-get -qq update && \
+    apt-get -qq -y install --no-install-recommends \
+        rsync \
+        curl \
+        unzip \
+        gnupg \
+        python3 \
+        python3-dev \
+        python3-pip \
+        build-essential \
+        libisal2 libisal-dev \
+        libdeflate0 libdeflate-dev
+
+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 -y google-cloud-cli=410.0.0-0
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64-2.8.10.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && \
+    ./aws/install && \
+    rm awscliv2.zip
+
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+RUN python -m pip install --upgrade pip --no-cache-dir && \
+    python -m pip install numpy==1.23.4 --no-cache-dir && \
+    python -m pip install pandas==1.5.1 --no-cache-dir && \
+    python -m pip install matplotlib==3.6.2 --no-cache-dir && \
+    python -m pip install stratocumulus==0.1.7 --no-cache-dir
+
+RUN tar -xzf /software/0.11.1.tar.gz -C /software && \
+    cd /software/cumulus_feature_barcoding-0.11.1 && make clean && make all && cd ../.. && \
+    rm -f /software/0.11.1.tar.gz
+
+RUN apt-get -qq -y remove gnupg && \
+    apt-get -qq -y autoremove && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /var/log/dpkg.log
+
+RUN chmod a+rx /software/*
+
+ENV PATH=/software:/software/cumulus_feature_barcoding-0.11.1:$PATH

docs/cellranger/feature_barcoding.rst

@@ -191,9 +191,9 @@ For feature barcoding data, ``cellranger_workflow`` takes Illumina outputs as in
 		  - "7.0.1"
 		  - "7.0.1"
 		* - cumulus_feature_barcoding_version
-		  - Cumulus_feature_barcoding version for extracting feature barcode matrix. Version available: 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0, 0.3.0, 0.2.0.
-		  - "0.11.0"
-		  - "0.11.0"
+		  - Cumulus_feature_barcoding version for extracting feature barcode matrix. Version available: 0.11.1, 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0, 0.3.0, 0.2.0.
+		  - "0.11.1"
+		  - "0.11.1"
 		* - docker_registry
 		  - Docker registry to use for cellranger_workflow. Options:
 

workflows/cellranger/cellranger_workflow.wdl

@@ -100,8 +100,8 @@ workflow cellranger_workflow {
 
         # 7.0.1, 7.0.0, 6.1.2, 6.1.1, 6.0.2, 6.0.1, 6.0.0, 5.0.1, 5.0.0
         String cellranger_version = "7.0.1"
-        # 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0, 0.3.0, 0.2.0
-        String cumulus_feature_barcoding_version = "0.11.0"
+        # 0.11.1, 0.11.0, 0.10.0, 0.9.0, 0.8.0, 0.7.0, 0.6.0, 0.5.0, 0.4.0, 0.3.0, 0.2.0
+        String cumulus_feature_barcoding_version = "0.11.1"
         # 2.1.0, 2.0.0, 1.2.0, 1.1.0
         String cellranger_atac_version = "2.1.0"
         # 2.0.2, 2.0.1, 2.0.0, 1.0.1, 1.0.0