download_pipeline.yml

name: Test successful pipeline download with 'nf-core pipelines download'

# Run the workflow when:
#  - dispatched manually
#  - when a PR is opened or reopened to master branch
#  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
on:
  workflow_dispatch:
    inputs:
      testbranch:
        description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
        required: true
        default: "dev"
  pull_request:
    types:
      - opened
      - edited
      - synchronize
    branches:
      - master
  pull_request_target:
    branches:
      - master

env:
  NXF_ANSI_LOG: false

jobs:
  download:
    runs-on: ubuntu-latest
    steps:
      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v2

      - name: Disk space cleanup
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
        with:
          python-version: "3.12"
          architecture: "x64"

      - name: Setup Apptainer
        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
        with:
          apptainer-version: 1.3.4

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install git+https://github.com/nf-core/tools.git@dev

      - name: Get the repository name and current branch set as environment variable
        run: |
          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}

      - name: Make a cache directory for the container images
        run: |
          mkdir -p ./singularity_container_images

      - name: Download the pipeline
        env:
          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
        run: |
          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
          --revision ${{ env.REPO_BRANCH }} \
          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
          --compress "none" \
          --container-system 'singularity' \
          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
          --container-cache-utilisation 'amend' \
          --download-configuration 'yes'

      - name: Inspect download
        run: tree ./${{ env.REPOTITLE_LOWERCASE }}

      - name: Count the downloaded number of container images
        id: count_initial
        run: |
          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
          echo "Initial container image count: $image_count"
          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}

      - name: Run the downloaded pipeline (stub)
        id: stub_run_pipeline
        continue-on-error: true
        env:
          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
          NXF_SINGULARITY_HOME_MOUNT: true
        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity,illumina --outdir ./results
      - name: Run the downloaded pipeline (stub run not supported)
        id: run_pipeline
        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
        env:
          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
          NXF_SINGULARITY_HOME_MOUNT: true
        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results

      - name: Count the downloaded number of container images
        id: count_afterwards
        run: |
          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
          echo "Post-pipeline run container image count: $image_count"
          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}

      - name: Compare container image counts
        run: |
          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
            final_count=${{ env.IMAGE_COUNT_AFTER }}
            difference=$((final_count - initial_count))
            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
            tree ./singularity_container_images
            exit 1
          else
            echo "The pipeline can be downloaded successfully!"
          fi