feat: add optional platform and token_env fields to input samplesheet #1
Workflow file for this run
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| name: Test successful pipeline download with 'nf-core pipelines download' | |
| # Run the workflow when: | |
| # - dispatched manually | |
| # - when a PR is opened or reopened to main/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: | |
| - main | |
| - master | |
| pull_request_target: | |
| branches: | |
| - main | |
| - master | |
| env: | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| configure: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} | |
| REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} | |
| REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} | |
| steps: | |
| - name: Get the repository name and current branch | |
| id: get_repo_properties | |
| run: | | |
| echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" | |
| echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" | |
| echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" | |
| download: | |
| runs-on: ubuntu-latest | |
| needs: configure | |
| 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@0b93645e9fea7318ecaed2b359559ac225c90a2b # 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: 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 ${{ needs.configure.outputs.REPO_LOWERCASE }} \ | |
| --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ | |
| --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ | |
| --compress "none" \ | |
| --container-system 'singularity' \ | |
| --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ | |
| --container-cache-utilisation 'amend' \ | |
| --download-configuration 'yes' | |
| - name: Inspect download | |
| run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} | |
| - name: Inspect container images | |
| run: tree ./singularity_container_images | tee ./container_initial |