# use the upstream nextflow container as a base image
ARG NEXTFLOW_VERSION
FROM public.ecr.aws/seqera-labs/nextflow:${NEXTFLOW_VERSION} AS build

COPY THIRD-PARTY /opt/
COPY LICENSE /opt/

FROM public.ecr.aws/amazonlinux/amazonlinux:2 AS final
COPY --from=build /usr/local/bin/nextflow /usr/bin/nextflow

RUN yum update -y \
  && yum install -y \
  curl \
  hostname \
  which \
  "java-11-amazon-corretto-headless(x86-64)" \
  unzip \
  jq \
  && yum clean -y all
RUN rm -rf /var/cache/yum

# install awscli v2
RUN curl -s "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "/tmp/awscliv2.zip" \
  && unzip -q /tmp/awscliv2.zip -d /tmp \
  && /tmp/aws/install -b /usr/bin \
  && rm -rf /tmp/aws*

ENV JAVA_HOME /usr/lib/jvm/jre-openjdk/

# invoke nextflow once to download dependencies
RUN nextflow -version

# install a custom entrypoint script that handles being run within an AWS Batch Job
COPY nextflow.aws.sh /opt/bin/nextflow.aws.sh
RUN chmod +x /opt/bin/nextflow.aws.sh

WORKDIR /opt/work
ENTRYPOINT ["/opt/bin/nextflow.aws.sh"]