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Dockerfile
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##############################################################################################################################
#
# This container includes all necessary components for initializing the Heritability Nextflow pipeline in Google Cloud
# Additional configuration options can be passed in via environment variables
#
##############################################################################################################################
# Base image includes Google Cloud SDK tools
FROM google/cloud-sdk:slim
# Install OpenJDK JRE for Nextflow
RUN apt-get update && apt-get upgrade -y && apt-get install -y --no-install-recommends openjdk-11-jre wget procps
LABEL Name="Heritability-NXF" Author="Katie Evans"
# Specify Nextflow version and mode
# (21.05.0-edge is the first version to support configuring which service account acts as pipeline-runner)
ENV NXF_VER=21.05.0-edge \
NXF_MODE=google \
NXF_EDGE=1
WORKDIR /heritability
# Run the Nextflow install script (version and mode must be piped in to bash during install
# or nextflow will initially download the latest version and only download and switch to NXF_VER when the container runs)
RUN NXF_VER=21.05.0-edge NXF_MODE=google NXF_EDGE=1 \
wget -qO- https://get.nextflow.io | bash
COPY heritability-nxf.sh /heritability/heritability-nxf.sh
COPY nextflow.config /heritability/nextflow.config
COPY main.nf /heritability/main.nf
COPY bin/* /heritability/bin/
# add nextflow and nemarun directory to te system path and make them executable
ENV PATH="/heritability:${PATH}"
RUN chmod +x /heritability/heritability-nxf.sh /heritability/nextflow