content: # Test build locally before making a PR
  #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
  
  # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
  FROM gitpod/workspace-base@sha256:77021d8db227d1f45a771a512ba54bdc36617eba313c964d12c51a49b0030bbd
  
  USER root
  
  # Install util tools.
  # software-properties-common is needed to add ppa support for Apptainer installation
  RUN apt-get update --quiet && \
      apt-get install --quiet --yes --no-install-recommends \
      apt-transport-https \
      apt-utils \
      sudo \
      git \
      less \
      wget \
      curl \
      tree \
      graphviz \
      software-properties-common && \
      add-apt-repository -y ppa:apptainer/ppa && \
      apt-get update --quiet && \
      apt-get install --quiet --yes apptainer && \
      wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
      bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
      rm Miniforge3-Linux-x86_64.sh && \
      apt-get clean && \
      rm -rf /var/lib/apt/lists/*
  
  # Set PATH for Conda
  ENV PATH="/opt/conda/bin:$PATH"
  
  # Add the nf-core source files to the image
  COPY . /usr/src/nf_core
  WORKDIR /usr/src/nf_core
  
  # Change ownership for gitpod
  RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
  
  # Change user to gitpod
  USER gitpod
  # Install nextflow, nf-core, nf-test, and other useful tools
  RUN conda config --add channels bioconda && \
      conda config --add channels conda-forge && \
      conda config --set channel_priority strict && \
      conda install --quiet --yes --update-all --name base \
      nextflow \
      nf-test \
      prettier \
      pre-commit \
      ruff \
      mypy \
      openjdk \
      pytest-workflow && \
      conda clean --all --force-pkgs-dirs --yes
  
  # Update Nextflow and Install nf-core
  RUN nextflow self-update && \
      python -m pip install . --no-cache-dir
  
  # Setup pdiff for nf-test diffs
  ENV NFT_DIFF="pdiff"
  ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
  ENV JAVA_TOOL_OPTIONS=
  