action.yml

name: snakemake

description: Run Snakemake on the repository

branding:
  icon: git-pull-request
  color: green

inputs:
  directory:
    description: Working directory for the execution
    required: true
    default: .test
  snakefile:
    description: Snakefile containing the workflow description
    default: Snakefile
  args:
    description: Additional Snakemake arguments to use
    required: false
    default: ''
  stagein:
    description: Additional steps to prepare the workflow for execution
    required: false
    default: ''
  task:
    description: Whether to run Snakemake or to generate a container image specification.
    required: false
    default: 'run'
  show-disk-usage-on-error:
    description: Whether to return the used disk space on failing.
    required: false
    default: false
  snakemake-version:
    description: Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
    required: false
    default: '*'
  install-apptainer:
    description: Install Apptainer (true/false)
    required: false
    default: false

runs:
  using: 'composite'
  steps:
    - name: Validate inputs
      if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
      shell: bash -el {0}
      run: |
        echo 'Invalid value for "task": "${{ inputs.task }}". Options: "containerize", "run".'
        exit 1

    - name: Install Apptainer
      if: ${{ inputs.install-apptainer == 'true' }}
      shell: bash -el {0}
      run: |
        if ! command -v apt-get &> /dev/null; then
          echo "Error: This action currently supports Apptainer installation only on Ubuntu runners"
          exit 1
        fi
        sudo apt-get update
        sudo apt-get install -y apptainer
    - name: Prepare .snakemake.environment.yaml
      shell: bash -el {0}
      run: |
        cat <<EOF > .snakemake.environment.yaml
        channels:
          - conda-forge
          - bioconda
          - nodefaults
        dependencies:
          - snakemake ==${{ inputs.snakemake-version }}
        EOF

    - name: Setup conda
      uses: conda-incubator/setup-miniconda@v3
      with:
        channels: conda-forge,bioconda
        channel-priority: strict
        miniforge-version: latest
        environment-file: .snakemake.environment.yaml
        activate-environment: snakemake

    - name: Display snakemake version
      shell: bash -el {0}
      run: snakemake --version

    - name: Run snakemake
      if: ${{ inputs.task == 'run' }}
      shell: bash -el {0}
      run: |
        snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }}
        if [[ "$?" -ne 0 ]]; then
          if [[ ${{ inputs.show-disk-usage-on-error }} = true ]]; then
              # return disk usage and space on failing
              df -h
              printf "disk usage working directory"
              du -h -d3 ${{ inputs.directory }}
          fi
          exit 1
        fi

    - name: Containerize snakemake
      if: ${{ inputs.task == 'containerize' }}
      shell: bash -el {0}
      run: snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize > Dockerfile