Dockerfile-nextflow

FROM debian:bullseye
LABEL maintainer="Tim Dudgeon<tdudgeon@informaticsmatters.com>"
# Note:     When run by the Data Manager the uid and gid
#           will be set according to the Project we're running against.
#           Consequently we cannot know in advance the user or group id
#           for execution, and so we must ensure the code runs
#           as any user.

RUN apt-get update &&\
 apt-get install -y --no-install-recommends\
 openjdk-11-jre-headless\
 curl\
 procps\
 git &&\
 apt-get clean -y
 
# Install nextflow. Releases are here: https://github.com/nextflow-io/nextflow/releases
RUN curl -Ls -o nextflow https://github.com/nextflow-io/nextflow/releases/download/v22.10.0/nextflow-22.10.0-all && \
    chmod 755 nextflow && \
    mv nextflow /usr/local/bin/

ENV HOME=/code
WORKDIR ${HOME}

COPY *.nf ./
COPY moldb/*.nf ./moldb/

COPY nf-processes ./nf-processes

# Adjust permissions for RunAsAnyUser
RUN chmod 777 ${HOME}