Add RSEM + refactor tests #51
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| NFT_VER: "0.9.2" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| filter: ["pipeline"] | |
| # filter: ["process", "workflow", "function", "pipeline"] | |
| profile: ["conda", "docker", "singularity"] | |
| shard: [1, 2, 3, 4] | |
| # shard: [1, 2, 3, 4, 5] | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFT_VER }} | |
| - name: Set up apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Cache pdiff | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| id: cache-pip-pdiff | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-pdiff | |
| - name: Install pdiff | |
| run: python -m pip install --upgrade pip pdiff cryptography | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Start summary | |
| id: print-test | |
| run: | | |
| echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "This \`${{ matrix.filter }}\` ${{ matrix.shard }}/5 shard was run on \`${{ matrix.profile }}\` | \`NXF_VER=${{ matrix.NXF_VER }}\`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| nf-test test \ | |
| --ci \ | |
| --dryRun \ | |
| --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ | |
| --shard ${{ matrix.shard }}/5 \ | |
| --changed-since HEAD^ \ | |
| --follow-dependencies \ | |
| --profile "+${{ matrix.profile }}" \ | |
| --filter ${{ matrix.filter }} \ | |
| | grep PASSED | cut -d "'" -f 2 | sed 's/^/- /' | sort -u >> $GITHUB_STEP_SUMMARY | |
| - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5" | |
| run: | | |
| nf-test test \ | |
| --ci \ | |
| --debug \ | |
| --verbose \ | |
| --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ | |
| --shard ${{ matrix.shard }}/5 \ | |
| --changed-since HEAD^ \ | |
| --follow-dependencies \ | |
| --profile "+${{ matrix.profile }}" \ | |
| --filter ${{ matrix.filter }} | |
| - name: Print success in summary | |
| if: success() | |
| run: | | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "All test(s) successfull :tada:" >> $GITHUB_STEP_SUMMARY | |
| - name: Print failure in summary | |
| if: failure() | |
| run: | | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "Some test(s) failed :cold_sweat:" >> $GITHUB_STEP_SUMMARY | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v4 | |
| if: success() || failure() # always run even if the previous step fails | |
| with: | |
| report_paths: "TEST-*.xml" | |
| - name: Clean up | |
| if: success() || failure() | |
| run: | | |
| sudo rm -rf /home/ubuntu/tests/ |