FROM eclipse-temurin:17-jdk AS build

WORKDIR /opt/nextflow

COPY . /opt/nextflow

RUN chmod +x ./gradlew

RUN ./gradlew clean assemble pack

RUN mkdir -p /tmp/nf-unpack /opt/nf-dist \
 && cd /tmp/nf-unpack \
 && jar xf /opt/nextflow/modules/nextflow/build/distributions/nextflow-26.04.0.zip \
 && cp -a nextflow-*/* /opt/nf-dist/ \
 && chmod +x /opt/nf-dist/bin/nextflow

RUN mkdir -p /tmp/nxf-home/plugins/nf-k8s-1.5.2 \
 && cd /tmp/nxf-home/plugins/nf-k8s-1.5.2 \
 && jar xf /opt/nextflow/plugins/nf-k8s/build/distributions/nf-k8s-1.5.2.zip

RUN mkdir -p /tmp/nxf-home/plugins/nf-amazon-3.9.0 \
 && cd /tmp/nxf-home/plugins/nf-amazon-3.9.0 \
 && jar xf /opt/nextflow/plugins/nf-amazon/build/distributions/nf-amazon-3.9.0.zip

FROM eclipse-temurin:17-jre

WORKDIR /opt/nextflow

COPY --from=build /opt/nf-dist /opt/nextflow
COPY --from=build /tmp/nxf-home /opt/nextflow/.nextflow

ENV PATH="/opt/nextflow/bin:${PATH}"
ENV NXF_HOME="/opt/nextflow/.nextflow"
ENV NXF_PLUGINS_DIR="/opt/nextflow/.nextflow/plugins"
ENV JAVA_OPTS="--add-opens java.base/java.nio.file.spi=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.util.concurrent=ALL-UNNAMED"

ENTRYPOINT ["/opt/nextflow/bin/nextflow"]